Susie Salmon is killed on December 6, 1973 by her family’s neighbor, George Harvey. Mr. Harvey lures Susie into a hole he dug in the cornfield. When she tries to leave he rips off her clothes, gags her with her hat and rapes her. He kills her, cuts her up, and puts her in a bag that he takes with him before he fills in the hole. He puts the bag with her body in a safe and takes the safe to the local sinkhole.
When Susie gets to heaven she observes her family. Susie soon realizes that everyone has different heavens that fit what each person wants. She is grateful that Len Fenerman, the detective assigned to her case, is helping them. Upon finding Susie’s elbow, the police search the cornfield and find the hole and some of Susie’s belongings. Len Fenerman delivers the news to the Salmons that there is too much blood in the earth and they believe Susie is dead. In heaven, Susie watches her family from her gazebo. She looks at a picture that her little brother Buckley drew. In the picture there is a thick blue line separating the earth and the sky; Susie thinks of this space as the Inbetween, and believes it really exists.
When Susie’s soul was leaving the earth, she accidentally touched a girl named Ruth Connors. Because of this experience, Ruth becomes fascinated with Susie’s life and her death. Susie watches a number of people on earth, including Ruth, Susie’s family and her crush Ray Singh. Susie recalls a picture she took of her mother, Abigail, where she is alone and staring out into the yard and has not yet taken on her daily role as mother and wife. Lindsey finds the photograph in Susie’s room. Susie’s father, Jack, smashes all of the model ships he made. Susie used to help him make the ships, and she breaks the Inbetween by casting her face into the shards of glass.
Not long after Susie’s death, Mr. Harvey decides to build a tent outside of his house. Jack Salmon sees him and offers to help. Jack gets the feeling that Mr. Harvey knows something about Susie’s murder, and suspects him. He tells Len Fenerman, who goes to Mr. Harvey’s house to interview him but does not find him suspicious.
On Christmas, a boy named Samuel Heckler comes to visit Lindsey. He gives her a necklace and they kiss. Susie remembers one day she was late to school and she sat with Ray in the scaffolding in the theater, but the entrance of Ruth Connors interrupted them and they did not kiss. Later that week, Ray kissed Susie by her locker. After Susie’s death, Ruth regularly walks the cornfield before school. Ray notices and joins her; they become friends. Jack Salmon goes to the Singhs’ to talk to Ray. There he meets Ray’s mother Ruana Singh, and he confides in her that he knows who killed Susie.
Grandma Lynn comes to town for Susie’s memorial. She brings some light back to the Salmon household. At the memorial Lynn points out George Harvey to Lindsey and she faints. That summer, Lindsey, Samuel and Ruth go to a camp for gifted students. There, Lindsey and Samuel lose their virginity together. The final competition at camp is how to complete the perfect murder.
Susie watches Mr. Harvey and can see into his childhood, when his mother left the family.
His house is exactly like hers, but more barren. He spends a lot of time making dollhouses. Jack Salmon hopes to find clues about Mr. Harvey and constantly calls the police station to report trivial facts about the man. Finally, Len Fenerman comes to their house and tells them they are no longer pursuing the investigation of Susie’s murder. That night Jack sees a light in the cornfield; he thinks it is Mr. Harvey so he goes out with a baseball bat. It turns out to be Susie’s friend and her boyfriend, and Jack gets beaten up and goes to the hospital. There, Abigail begins an affair with Len Fenerman. Susie knows that Abigail never wanted to be a mother, and she is trying to find a way to escape from Susie’s death by having this affair.
When Jack gets home his leg is still stiff. Abigail becomes absorbed in her role as mother yet she distances herself from her children. Lynn comes to visit on Thanksgiving and notices something is different with Abigail, but realizes she can only support her in whatever she decides to do.
Lindsey starts to share her father’s suspicion of George Harvey so she breaks into his house and finds a drawing of the hole where he killed Susie. Mr. Harvey comes home and Lindsey narrowly escapes out the window. Mr. Harvey calls the police to report a break-in. Meanwhile, Abigail has met up with Len Fenerman at the mall and they consummate their affair. That night George Harvey leaves town, and later Len realizes he missed his chance to catch him.
The one-year anniversary of Susie’s death arrives, and some of her classmates hold a service for her in the cornfield. Abigail does not want to go, but Jack, Buckley and Lindsey go. The following summer Abigail leaves the family and ends up working at a winery in California. Grandma Lynn comes to stay with Jack to help him with the kids and the house. Buckley gets older, and decides to build a fort in the back yard to commemorate Susie. Len Fenerman now believes that George Harvey committed the murder but he cannot find him; in other states, clues begin to link him to other murders.
Lindsey and Samuel graduate from college and decide they want to get married and move into an old house they found. Not long afterwards, Jack has a heart attack and has to go to the hospital. Abigail comes back for the first time in over five years. She realizes she is still in love with Jack and slowly decides she will stay.
Ruth Connors comes back to her hometown because she wants to see the sinkhole before developers close it up. She asks Ray to go with her. When they are there, Susie is watching and manages to break the Inbetween and live in Ruth’s body for a few hours. During this time, she makes love to Ray Singh.
The next day, Jack Salmon goes home with his family. Ray and Ruana Singh come over for a visit. While watching them Susie realizes she is grateful for the relationships that grew up in her absence—she refers to these as the lovely bones. Susie decides she is done watching the living, and knows they can move on.
After Susie leaves them, Abigail and Jack stay together in the house and openly talk about Susie when they think of her. Susie goes to a new place in heaven where she has things she never dreamed of in her first, smaller, heaven. There, Susie watches Mr. Harvey die by falling into a ravine. He was never caught. Lindsey and Samuel get married and have a daughter they name Abigail Suzanne. Susie knows she never really grew up but feels she almost has.