Scorsese has been criticised by a number of Marvel alumni, including Samuel L. Jackson, Karen Gillan, and "Guardians of the Galaxy" director James Gunn, for saying the superhero films make him think of "theme parks" rather than cinematic excellence.
However, Downey, Jr. isn't angered by the remarks, as he told SiriusXM radio host Howard Stern that even he struggles to comprehend how huge Marvel movies have become.
"I'll tell you the truth, I didn't expect (the Marvel Cinematic Universe) to become what it became and it is this very large, multi-headed Hydra at this point," he said. "I've always had other interests, and according to Scorsese, it's not cinema so I have to take a look at that, you know?"
The 54-year-old actor disagreed with "The Irishman" filmmaker saying Marvel blockbusters play well "in theatres" but admitted there maybe something to the idea that the runaway success of comic book movies had crowded out some more artful films.
"By the way, there's a lot to be said about how these genre movies - and I was happy to be a part of the 'problem,' if there is one - denigrated the art form of cinema," he added. "When you come in like a stomping beast and you eliminate the competition in such a demonstrative way, it's phenomenal."
Although he disagrees with Scorsese, saying he thinks his comment "makes no sense," Downey, Jr. explained: "I appreciate his opinion because I think, it's like anything, we need all of the different perspectives so we can come to centre and move on."