Pep Guardiola's side beat PSG over two legs to progress to last season's UEFA Champions League final, before going down 1-0 to Chelsea in the showpiece final.
The two sides will meet again in the group stage on Wednesday (AEST), with PSG having drawn its first match, at Club Brugge, while City defeated RB Leipzig 6-3.
It is a headline fixture of the group stages, with PSG's star-studded front line going up against the Premier League champion.
However, there is a fitness doubt over Messi, who was absent for PSG's dramatic 2-1 Ligue 1 win over Metz in midweek because of a knee injury.
Messi will also miss Sunday's (AEST) Ligue 1 encounter with Montpellier, but Pochettino said it is too early to rule the 34-year-old out for the match against City.
"Leo has started to run today and as you have seen in the medical update we are going to assess him and we hope he improves," Pochettino said on Saturday (AEST).
"On Sunday [Monday AEST], we hope we will be able to give a positive update. We hope everything goes well and he will be available again.
"Yes, we hope he can play. We have to be cautious and we have to see how he evolves in the next few days."
Messi has played just three games since his stunning departure from Barca and has yet to find the net for PSG.
He hit the crossbar against Brugge and then also hit the woodwork with a long-range free-kick against Lyon on Monday (AEST) before he was substituted.
Mauro Icardi scored a late winner against Lyon, and Pochettino has been delighted with the striker's form this season despite the former Inter Milan man missing a chunk of games through injury.
"Mauro Icardi, he is player who contributed a lot until his injury," Pochettino said.
"He recovered and has made a big impact. He scored against Lyon and of course, he offers us an alternative in our attacking play."