Messi and Ronaldo have won a record five Ballon d'Or awards apiece, while the pair are the all-time leading goalscorers for their respective clubs.
But Silva – who is set to come up against Ronaldo and titleholders Madrid in the Champions League last 16 – spoke in favour of Messi.
"It's harder to defend against Leo Messi than Cristiano Ronaldo," Silva said. "Cristiano deserved to win everything he's won in his career. This year is a bit harder for him but it's not over yet. He could still win the next Ballon d'Or.
"The little difference between them is that Messi, with the ball, one on one, or even against two, is difficult to stop."
Silva added: "They are both players who do incredible things, like Neymar, for example."
Ligue 1 leaders PSG will travel to Madrid's Santiago Bernabeu for the first leg of their last-16 tie on February 14.