Joaquin Rafael Bottom is the third of five children, all with equally interesting names, including River (1970–1993), Rain (1973), Liberty (1976), Summer, and a half-sister Jodean.

After Joaquin's parents, John Lee and Arlyn Bottom, married in 1969, the couple joined the religious cult the Children of God and traveled around South America. But they soon became disenchanted with the cult and moved back to the U.S. in 1978, where they changed their last name to "Phoenix" to symbolize "new beginning."

Around this same time, a young Joaquin began calling himself "Leaf," desiring to have a similar nature-related name like his siblings. In a past Jay Leno interview, Joaquin said he had originally called himself "Antleaf" as a child.

Leaf would become the name he would use as a child actor until, at age 15, he changed it back to Joaquin.