Molina married fellow chemist Luisa Y. Tan in July 1973. They had met each other when Molina was pursuing his PhD at the University of California, Berkeley. They moved to Irvine, California in the fall of that year. The couple divorced in 2005. Luisa Tan Molina is now the lead scientist of the Molina Center for Strategic Studies in Energy and the Environment in La Jolla, California. Their son, Felipe Jose Molina, was born in 1977. Molina married his second wife, Guadalupe Álvarez, in February 2006.
Molina died on 7 October 2020, aged 77, due to a heart attack.