In 1973, 14-year-old Susie Salmon takes her usual shortcut home from her school through a cornfield in Norristown, Pennsylvania. George Harvey, a 36-year-old neighbor who lives alone and builds doll houses for a living, persuades her to have a look at an underground den he has recently dug in the field. Once she enters, he rapes and murders her, then dismembers her body, putting her remains in a safe that he dumps in a sinkhole. Susie's spirit flees toward her personal heaven, and in doing so, rushes past one of Susie's classmates and social outcast, Ruth Connors.
The Salmon family at first refuses to believe that Susie is dead, until a neighbor's dog finds Susie's elbow. The police talk to Harvey, finding him strange but seeing no reason to suspect him. Susie's father, Jack, begins to suspect Harvey, a sentiment his surviving daughter Lindsey comes to share. Jack takes an extended leave from work. Meanwhile, another of Susie's classmates, Ray Singh, who had a crush on Susie in school and had made plans to go out with her a few days before her murder, develops a relationship with Ruth, as they are drawn together by their connection with Susie.
Later, Len Fenerman, the detective assigned to the case, tells the Salmons the police have exhausted all leads and are dropping the investigation. That night in his study, Jack looks out the window and sees a flashlight in the cornfield. Thinking it is Harvey returning to destroy more evidence, he runs out to confront him, armed with a baseball bat. The figure is not Harvey, but Clarissa, Susie's best friend who is dating Brian, one of Susie's classmates. As Susie watches in horror from heaven, Brian—who was going to meet Clarissa in the cornfield—nearly beats Jack to death, and Clarissa breaks Jack's knee. While he recovers from knee replacement surgery, Susie's mother, Abigail, begins cheating on Jack with the widowed Fenerman.
Trying to help her father prove his suspicions, Lindsey sneaks into Harvey's house and finds a diagram of the underground den, but is forced to leave when Harvey returns unexpectedly. The police do not arrest him, however, which enables him to flee from Norristown. Later, evidence is discovered linking Harvey to Susie's murder as well as to those of several other girls. Meanwhile, Susie meets Harvey's other victims in heaven and sees into his traumatic childhood.
Abigail leaves Jack and eventually takes a job at a winery in California. Her mother, Grandma Lynn, moves into the Salmons' home to care for Buckley (Susie's younger brother) and Lindsey. Eight years later, Lindsey and her boyfriend, Samuel Heckler, become engaged after finishing college, find an old house in the woods owned by a classmate's father, and decide to fix it up and live there. Sometime after the celebration, while arguing with his son Buckley, Jack suffers a heart attack. The emergency prompts Abigail to return from California, but the reunion is tempered by Buckley's lingering bitterness for her having abandoned the family for most of his childhood.
Meanwhile, Harvey returns to Norristown, which has become more developed. He explores his old neighborhood and notices the school is being expanded into the cornfield where he murdered Susie. He drives by the sinkhole where Susie's body rests and where Ruth and Ray are standing. Ruth senses the women Harvey has killed and is physically overcome. Susie, watching from heaven, is also overwhelmed with emotion and feels how she and Ruth transcend their present existence, and the two girls exchange positions: Susie, her spirit now in Ruth's body, connects with Ray, who senses Susie's presence and is stunned by the fact that Susie is briefly back with him. The two make love as Susie has longed to do after witnessing her sister and Samuel. Afterwards, Susie returns to heaven.
Susie moves on into another, larger part of heaven, occasionally watching earthbound events. Lindsey and Samuel have a daughter together named Abigail Suzanne. While stalking a young woman in New Hampshire, Harvey is hit on the shoulder by an icicle and falls to his death down a snow-covered slope. At the end of the novel, a Norristown couple finds Susie's charm bracelet but don't realize its significance, and Susie closes the story by wishing the reader "a long and happy life".