The Argentina star bagged a brace in Saturday's 6-0 Primera Division home win over Rayo Vallecano to take him to 228 La Liga goals in just 263 games.
Messi is also just six behind Raul's 71 in the all-time Champions League goalscorers list and heads into the first leg of their last-16 tie in superb form with five goals in his last three matches.
And although Pellegrini admits he has never seen the 26-year-old have a bad game, he hopes he underperforms at the Etihad.
"I have never seen Messi play badly. He's either excellent or great. We hope to face the worst Messi - not the great one," admitted the City boss.
"It is difficult to stop him, it is. Without doubt, it's very difficult because he's the top player of the world and he has a lot of different qualities.
"He has speed, good balance and a good finish. He's very important, but I don't think Barcelona is Messi.
"You can have a lot of other players who will also decide the game as well, so it's important to play as a team, defending and attacking."