Spurs take on Manchester United on Sunday, hoping to extend a difficult period for their opponents, who have managed only one win in eight Premier League matches.
Mourinho, the self-proclaimed Special One, sees his United team six points behind Tottenham and already 13 points adrift of table-toppers Chelsea ahead of the game.
Pochettino, however, believes the Portugese needs more time at his new club.
"For me, he is the Special One and will always be the Special One," Pochettino said.
"For me, he was a reference when I started my career at Espanyol
He was always very kind to me and opened his door.
"I always assess my colleagues and try to be objective - I really believe he is one of the best.
"Sometimes you struggle a bit - it's not easy to arrive at a new club, set up ideas and philosophy but, for me, he was, is and will be one of best managers in football history."
Mourinho was sacked by Chelsea midway through last season after a poor start to their title defence and he has cut a frustrated figure during the current campaign.
He was fined for comments made about referee Anthony Taylor in October, sent off against Burnley later that month and last week received a charge of improper conduct for kicking a bottle against West Ham.
"You get frustrated from the touchline but he doesn't do different things from me or another manager," Pochettino said.
"I like Mourinho, I have a good relationship with him
But I try to be objective too and his behaviour is no different from another manager - but because he is the Special One, sometimes people, referee, the media focus on him.
"But if you compare (him) with another manager, who behaves worse than him, they are not in the focus because they are not the Special One like him."
Pochettino was reportedly on the shortlist to replace Louis van Gaal at United last summer but Mourinho was chosen and instead the Argentinian signed a new five-year contract at White Hart Lane.
Tottenham defender Jan Vertonghen admits the players were relieved when Pochettino committed his future to the club.
"When the rumours were getting bigger we were always worried, especially with this manager," Vertonghen said.
"If I was Man United, I would have tried to take him from us, especially when you see what he can do to a team
The team is very happy he stayed."
Tottenham will be without Erik Lamela on Sunday as the midfielder is still in Argentina attending to his brother, who is in hospital
Vincent Janssen is also unavailable with an ankle injury.
Toby Alderweireld, however, is in line to make his first start in eight weeks following a knee problem
The defender came off the bench in the second half of Spurs' Champions League victory over CSKA Moscow on Wednesday.
"We need to decide tomorrow if he is in good form to play 90 minutes but we are happy after two months out how he came back," Pochettino said.
"It was good for him to feel the competition again against CSKA for 25 minutes."
Source : PA