United boss David Moyes has hinted Rooney will be backup next season to Robin van Persie.
Mourinho said: "Players who want to go to their national team and play for their country, normally they must be first-choice players for their clubs and be playing regularly.
"That's the big motivation if you are thinking about playing at the World Cup.
"If they want to go to the World Cup and they're second choice at their club, then they're in trouble. I think it's a crucial year for them.
"I know many national team coaches are worried because they want players to play regularly for their clubs."