Pochettino's Saints will be trying to stop Rooney at Old Trafford on Saturday, and they travel north with the best defensive record in the Premier League this season.
They have conceded just twice so far, but Pochettino says on Saturday they will be up against a striker on a par with the two players generally acknowledged as the best in the world.
The United striker has been in fine form this season for club and country, and he has now scored nine goals in his last 10 matches for England.
"I was speaking about it with my staff and we were saying he is the type of football player who is able to understand what is needed and what's required of him at every single phase of the game," Pochettino said.
"He's a fantastic player that's able to play up front, to drop a bit higher in the pitch. He's a fantastic footballer.
"I honestly rate him as high as Cristiano Ronaldo and Messi. I have a great admiration for how he is as a football player.
"I think he's an amazingly talented football player and I rate him as high as those two players."