Mourinho's summer appointment at Old Trafford raised questions over the future of Mata after the Portuguese boss had sold the playmaker to United from Chelsea in 2014.
However, the 28-year-old has established himself as an important part of Mourinho's team so far this season, and the manager believes that is down to the differing philosophies between the two clubs.
"The football I want to play and the profile at Man Utd and what I want to do in this club is completely different situation," Mourinho told reporters.
"In my project at Chelsea he was a good player. In my project at Man Utd he is a very good player. There are big differences. At Man Utd I have no players to play transitional football.
"We are trying to play in a different way. It is very adapted to his qualities. He has found a natural habitat for his football."
Mata has scored two goals in four Premier League starts so far this season.