Harvest Home is narrated in the first person by Ned Constantine, and describes events surrounding himself, his wife Beth, and their daughter Kate. Fed up with life in New York City, the family relocates to the country, where Ned can pursue an artistic career. After months of intermittent searching for a suitable new home, they discover a geographically isolated village in Connecticut named Cornwall Coombe. The village seems an idyllic farming community that offers all that Ned and Beth have been seeking. They express interest in an abandoned three-hundred-year-old house, and they are contacted some weeks later by the Dodds, who live next door to the house, and who tell them that it is for sale. The Constantines buy and renovate the house and move to Cornwall Coombe.
The opening chapters describe several matters in innocent detail, including the past marital difficulties of Ned and Beth, now apparently resolved; the moody Kate's serious, potentially life-threatening asthma, in part a psychosomatic reaction to those marital troubles; and, most importantly, the eccentricities of life in Cornwall Coombe. The villagers adhere stubbornly to what they call "the old ways", eschewing modern agricultural methods and limiting contact with the outside world. The villagers celebrate a number of festivals that revolve around the cultivation of corn, which is their chief product. The most important rite is Harvest Home, which takes place at the conclusion of the crop growing year. While the villagers are ostensibly Christian, Ned gradually becomes aware of the paganism that underlies life in Cornwall Coombe, particularly its rituals.
The Constantines befriend the Dodds. Maggie Dodd, an educated woman who left Cornwall Coombe but later returned with her husband, Robert, an outsider. Maggie is the church organist. Robert Dodd, totally blind, is a retired college professor. Other prominent villagers who become friends with the newcomers are Worthy Pettinger, a young man who disdains the old ways and wants to go to agricultural college; Justin Hooke, who serves as the current year's ceremonial "Harvest Lord", and his wife Sophie, whom Justin has chosen to be his "Corn Maiden" in the approaching "Corn Play"; Jack Stump, a local itinerant peddler, only recently arrived; and Mary Fortune, a widowed herbalist and midwife, and the town's most influential resident.
During a late summer festival, known as Agnes Fair, Ned first begins to sense something sinister. After most of the festivities are over, Ned hears a horrible cry and beholds a strange spectacle: Missy Penrose, a young girl regarded by the farmers as an oracle, stands over a newly slaughtered sheep and touches her blood-drenched hands to Worthy's face. Ned learns that this means Worthy has been chosen to be the "Young Lord", who will succeed Justin as Harvest Lord when Justin's seven-year term ends later that year. Worthy is the only one unhappy at this development.
Jack Stump reports that he has seen a ghost in Soakes' Lonesome, a local forest named for the family of moonshiners who live within. Ned sees a strange apparition one night, and later finds a skeleton hidden deep within the woods. Worthy decides secretly to leave the village with Ned's help rather than become Harvest Lord. Jack disappears. Ned grows preoccupied with the mysterious death of Grace Everdeen fourteen years earlier: she is buried in unhallowed ground, and the locals still occasionally say harsh but unspecific things about her.
Ned finds a primitive corn dolly in Justin's fields. The Widow Fortune succeeds in resuscitating Kate and saving her from certain death during an asthma attack; her herbal remedies apparently cure Kate of her asthma. Ned, under the influence of the Widow's mead, believes he sees the Harvest Lord and Corn Maiden trysting in a neighboring cornfield. During a harvest service in church, Worthy loudly curses the corn and "the Mother" and then flees. The community is scandalized. Worthy's parents are ostracized by the villagers. Jack Stump is found mutilated, having had his tongue cut out and mouth sewn shut in apparent retribution for trespassing into Soakes' Lonesome.
Ned becomes more intent on unravelling the village's secrets while his personal life goes awry. Tamar Penrose, the postmistress, seduces Ned, whose resistance weakens as he tries to learn more about Missy and her abilities. Ned learns that the women of Cornwall Coombe practice pagan fertility rites connected to the earth mother. Tamar reveals that she served as Corn Maiden fourteen years ago, and that Missy was conceived as a result. Grace Everdeen, originally slated to be Corn Maiden for her fiancé Roger Penrose, had developed a disfiguring disease. When she was replaced by Tamar, Grace cursed the corn. Drought followed, for which Grace was blamed.
At the end of the harvest, the villagers come together for a Husking Bee, a riotous party marking the conclusion of the growing season. Ned and other male villagers drink heavily as part of the festivities. During the Husking Bee, the villagers put on the Corn Play, a symbolic fertility rite that foreshadows what will happen at Harvest Home a few nights later. Ned watches stuporously as the women perform a barefoot pagan dance. When the women draw Kate into their circle, Ned furiously breaks into the dance to pull her back out but the villagers cast him into the street and pelt him with corn cobs for interfering in the ritual.
The Constantines' marriage has begun to unravel again. Beth had hoped to have another child, but Ned learns that he is sterile. Beth, aware of Tamar's designs on him, grows distrustful of Ned. Ned dislikes and distrusts the rapacious Tamar, but finally has sex with her in which she dominates him, symbolizing the ancient homage that men are forced to pay to the earth goddess. Robert Dodd explains to Ned the matriarchal pagan fertility religions of antiquity, and advises Ned to steer clear of Harvest Home at all costs: previous discovery of the secrets of these rites by any man has always resulted in dire consequences, which Dodd has suffered himself. Dodd removes his dark glasses showing that his blindness is the result of his eyes having been gouged out in retaliation for observing the sacred ritual, but Ned disregards his warnings.
Ned's rage at Tamar is further fueled by the discovery that Tamar was involved in the mutilation of Jack Stump. The villagers wanted to prevent him revealing that the skeleton in the woods— the same skeleton that Ned later discovered — belonged to Grace Everdeen, who had resisted the pairing of her fiancé with Tamar at Harvest Home fourteen years earlier, and was killed after arriving and disrupting the rites. The villagers, having learned Worthy's location from a letter he sentto Ned, which was steamed open by Tamar, the postmistress, send a posse to find him. He is returned home and killed. They initially hang his corpse in a field as a scarecrow, and later fling it into a massive bonfire on Kindling Night. On the day of Harvest Home, Justin's wife Sophie Hooke, the newCorn Maiden, hangs herself. She is denied burial in consecrated ground on the orders of the Widow Fortune. Ned denounces the villagers at the church and the widow, a revered high priestess, declares him an outcast. Missy instructs the gathered villagers to confine Ned.
Ned escapes from the building in which he is imprisoned via a secret passageway to the church. There, the village women have chosen the new Corn Maiden who is heavily veiled; Ned believes she is Tamar. She departs with the other women and Justin for the Harvest Home ritual. Ned races to the forest clearing ahead of them, determined despite Dodd's advice to discover what happens there. He watches the women play out the rites, which includes the copulation of the Harvest Lord with the Corn Maiden to symbolically ensure the fertility of the Mother. To Ned's horror, the new Corn Maiden is not Tamar, it is Beth. Ned cries out, alerting the women to his presence. He is forced to watch while Justin and Beth complete their intercourse, finally learning why Worthy had tried to escape and why Sophie killed herself: Tamar cuts Justin's throat with a sickle as he climaxes, spilling his blood onto the ground throughout the clearing. The villagers allowed Ned's family to settle here in order to bring new blood, Beth's and Kate's, into Cornwall Coombe. Ned tries to escape but the women surround him and render him blind and mute.
Months later, the blind, dependent Ned learns both that Beth is pregnant and that Kate is destined to be the next Corn Maiden.