Mourinho was sent off for kicking a water bottle down the touchline against West Ham United at Old Trafford last month, and served a one-match FA ban for improper conduct.
The suspension was his second of the season, but Pochettino said Mourinho was being singled out while other managers were going unpunished because they attracted less scrutiny.
“I have a good relationship with (Mourinho) but I try to be objective too,” Pochettino told a news conference on Friday.
“I think his behaviour is no different than others but because he is the 'Special One' sometimes the people are focused on him, the referee is focused on him, the media is focused on him.
“But if you compare him with another manager, and another manager behaves worse than him, they are not in the focus because maybe they are not the 'Special One' like him.”
United are sixth in the table, six points behind fifth-placed Tottenham, but Pochettino said his team would have no significant advantage because of United's involvement in the Europa League.
Tottenham, who beat CSKA Moscow in the Champions League on Wednesday to qualify for the last 32 in Europe's second-tier competition, have one more day to recover than United, who beat Zorya Luhansk 2-0 away in the Europa League on Thursday.
“When you play against a team like Manchester United they have a very good squad, a strong squad, and they can rotate players. That is their decision, Jose Mourinho's decision,” Pochettino added.
“For me he is the 'Special One' and always will be the 'Special One'... Some periods in football sometimes you struggle a little bit because it is not easy to arrive at a new club, a big club and set your ideas, your philosophy.
“But for me he was and he is and will be one of the best managers in football history.”
Spurs centre back Toby Alderweireld is in line for a first league start since October after returning to fitness, while full back Ben Davies, who last played at the start of November, is also available for selection after injury.
Striker Vincent Janssen (ankle) is unavailable, while forward Erik Lamela, who has not played since October because of a hip problem, is in Argentina this week for personal reasons.
Original source: Mourinho is always under scrutiny, says Pochettino