Boy, Snow, Bird is a twist on the classic fairytale Snow White set in the 1950s. A 20-year-old white woman named Boy Novak runs away from her abusive father in New York City and eventually meets a widowed jewelry designer and former history professor named Arturo Whitman. Boy and Arturo get married, settle down in small-town Massachusetts, and Boy becomes infatuated with her beautiful, poised, perfect stepdaughter, Snow, who's doted upon by her family, especially her grandparents. Arturo also has a sister, Clara, but she's been shunned by her family.
Boy and Arturo have a daughter, Bird, who is clearly African-American, revealing that Arturo, Snow, those doting grandparents, and Snow's deceased mother are/were all light-skinned African Americans who have been passing as white for their entire lives. Boy also learns that Clara was cast out of her family because she was too dark-skinned to pass.
Clara offers to raise Bird as her own, but Boy, instead, sends Snow to live with Clara, for fear of what having Snow around might do to Bird. Bird's brought up an as only child, and Arturo visits Snow two times a month. Bird finds letters written to Boy by Snow, begging to come home. Then she finds a letter from Snow to her and responds.
The two girls continue conversing in secret, and when Boy finds out, she allows Snow to visit. The Whitmans are also paid a visit by Boy's father, Frank, who tries to kidnap Bird, and then leaves, presumably for good. Thanksgiving finds the entire family, including Snow, Clara, and Clara's husband, John, together at last. Boy asks for Snow's forgiveness.
Boy's friend Mia shows up on Boy's doorstep and confesses that she's the one who gave Frank their address. Mia's a journalist, and she was working on an article that involved Boy's absent mother. It's revealed that Boy's father, Frank, was actually Boy's mother, Frances. Before becoming Frank, Frances was a lesbian and a Ph.D. candidate. After being raped by an acquaintance because she was gay, Frances became pregnant and transitioned to a man: Frank. Mia told Frank to tell Boy the truth before she published her article, and that's why Frank came to Boy's house. Boy, Bird, and Snow decide to accompany Mia to New York to see Frank——and hopefully Frances, too.