The BloodRayne director told Screen Junkies that he "hated" Malick's long-awaited film, which won the Palme d'Or at this year's Cannes Film Festival.
Boll said: "I totally hated that movie because I feel as a filmmaker that besides the fact that Terrence Malick did some great visuals on some movies, also on The New World, like the opening of that movie was really good but then he completely lost it.
"I think Tree of Life is a piece of s**t. Totally, and I think Sean Penn is ridiculous in it, like walking around in the elevator. It's nothing. This is the thing. It's so overrated because it's Terrence Malick."
Watch a trailer for The Tree of Life below:
Boll continued: "Same as Lars von Trier's movies. I like Breaking the Waves. After that was all crap. The thing is he gets all the Hollywood stars, 'Oh, I want to work with him' and they don't know what kind of retard he is.
"I think the same with Terrence Malick. I think Terrence Malick is one of the overrated directors of all time."
Boll added: "His other movies you get the feeling he tries to tell a story and cannot do it. But this was poor experimental. You cannot tell me you were not bored to death while you watched The Tree of Life."
Boll has previously insulted Michael Bay and was given a lifetime dishonour prize at the Golden Raspberry Awards in 2009.
> Read our review of Terrence Malick's The Tree of Life
> Read our review of Lars von Trier's Melancholia