Messi was La Liga's top scorer with 50 goals last season, four more than Ronaldo, and capped his season by winning a third Ballon d'Or title.
"For me, the best player of a season must be one that won. What (Ronaldo) did helped the team to win something big and I don't think in the history of the Ballon D'Or, one player won it without winning a big thing," Mourinho told ESPN.
"So I don't think Messi without winning the Champions League, without winning the Spanish League, how can he be the Ballon D'Or?"
Barcelona finished second behind Real Madrid who set records for most La Liga wins in a season with 32, most goals scored (121) and best goal difference (plus-89) en route to a first league title in four years, Sport24 reports.
Mourinho also remained confident for the new season despite no new signings.
"The team is really full of talent and we have lots of solutions and we can play in different ways, in different systems, in different philosophies. So, what I have in my hands in terms of human capital, human resources is very, very hard," he said.
Real Madrid and Barcelona will play in the Spanish SuperCup on August 23 and 29, with the first of two La Liga clashes set for October 7. (ANI )