The German outfit lost on penalties in the final of the competition last season, but face the La Liga club in the semi-finals on Tuesday.
The Argentine has warned his teammates that they must be at their best if they are to knock out the Bundesliga champions.
"Any opponent in these semi-finals was going to be tough, but Bayern this year are very, very good. They have been playing at a very high level and scoring a lot of goals," Messi told The Times of India.
"After what happened at the end of 2012, when they lost the final at their own ground to Chelsea, I think they have even more desire to go for the title this time. And Bayern are stronger this year than last in my opinion.
"Right now, we do not speak of the final but only about Bayern. And if we get to the final we do not care who we play as long as we are there again. But it is indisputable that a final at Wembley against Real Madrid would be a special game for many things and many people. If it is Real in the final it will be a great show, that's for sure."
The first leg gets takes place at the Allianz Arena on Tuesday night.