On December 6, 1973, 14-year-old Susie Salmon takes her usual shortcut home from her school through a cornfield in Norristown, Pennsylvania. George Harvey, her 36-year-old neighbor, a bachelor who builds doll houses for a living, persuades her to look at an underground kid's hideout he constructed in the field. Once she climbs into the hideout, he rapes and murders her, then dismembers her body and puts her remains in a safe that he dumps in a sinkhole, along with throwing her charm bracelet into a pond. Susie's spirit flees toward her personal Heaven, and in doing so, rushes past her classmate, social outcast Ruth Connors, who can see Susie's ghostly spirit.
The Salmon family initially refuses to believe that Susie is dead, until a neighbor's dog finds Susie's elbow. The police talk to Harvey, finding him odd but not suspicious. Susie's father, Jack, gradually suspects Harvey. Jack's surviving daughter, Lindsey, eventually shares this sentiment. Jack takes an extended leave from work. Meanwhile, another of Susie's classmates, Ray Singh, who had a crush on Susie in school, develops a friendship with Ruth, drawn together by their connection with Susie.
Later, Detective Len Fenerman tells the Salmons that the police have exhausted all leads and are dropping the investigation. That night, Jack peers out of his den window and sees a flashlight in the cornfield. Believing Harvey is returning to destroy evidence, Jack 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 Jack recovers from knee replacement surgery, Susie's mother, Abigail, begins cheating on Jack with the widowed Det. 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 unexpectedly returns. The police do not arrest Lindsey for breaking and entering. Harvey flees from Norristown. Later, evidence is discovered that links Harvey to Susie's murder as well as 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. Abigail's 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 to another, larger part of Heaven, but occasionally watches 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 into the ravine below. 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".
