Molina received numerous awards and honors, including sharing the 1995 Nobel Prize in chemistry with Paul J. Crutzen and F. Sherwood Rowland for their discovery of the role of CFCs in ozone depletion.
Molina was elected to the United States National Academy of Sciences in 1993.
He was elected to the United States Institute of Medicine in 1996, 
and The National College of Mexico in 2003. 
In 2007, he was elected to the American Philosophical Society. He was also a member of the Mexican Academy of Sciences.
Molina was a fellow of the American Association for the Advancement of Science and co-chaired the 2014 AAAS Climate Science Panel, What We Know: The reality, risks and response to climate change.
Molina won the 1987 Esselen Award of the Northeast section of the American Chemical Society, the 1988 Newcomb Cleveland Prize from the American Association for the Advancement of Science, the 1989 NASA Medal for Exceptional Scientific Advancement and the 1989 United Nations Environmental Programme Global 500 Award. In 1990, The Pew Charitable Trusts Scholars Program in Conservation and the Environment honored him as one of ten environmental scientists and awarded him a $150,000 grant.
In 1996, Molina received the Golden Plate Award of the American Academy of Achievement. He received the 1998 Willard Gibbs Award from the Chicago Section of the American Chemical Society and the 1998 American Chemical Society Prize for Creative Advances in Environment Technology and Science. In 2003, Molina received the 9th Annual Heinz Award in the Environment.
Asteroid 9680 Molina is named in his honor.
On 8 August 2013, US president Barack Obama announced Molina as a recipient of the Presidential Medal of Freedom, saying in the press release:
Mario Molina is the recipient of the Lifetime Achievement Award (Champions of the Earth) in 2014.
On 19 March 2023, Molina was the subject of a Google Doodle in Mexico, the United States, Brazil, India, Germany, France, and other countries.