The Brazilian believes the frustration at Real Madrid is reminiscent of the Portuguese's Nerazzurri spell and praised current PSG coach Carlo Ancelotti.
The coach is set to take charge of his final Blancos game on Saturday following a turbulent season which has seen him fall out with a number of players, most notably club captain Iker Casillas.
Thiago Motta, who now plays for Paris Saint-Germain, revealed that Mourinho's spell at San Siro was also plagued by problems behind the scenes, but believes he was helped by the press being kept from finding out about from it.
"I'm familiar with the agitation in the Madrid dressing room," the 30-year-old told Onda Cero. "Maybe it's a strategy of his, because the same thing happened to us at Inter.
"It was different, because there wasn't so much talk [in the press] - things did not leave the dressing room as much."
Thiago Motta had kinder words to say about his current boss at PSG, Carlo Ancelotti, whose man management skills he has praised following a season which has seen the club win Ligue 1.
The Brazilian added: "He's a great coach. He's done such a great job; we have a phenomenal atmosphere in the dressing room.
"Out of all of the coaches that I've had, he's different one-to-one. He's more natural."