Your first sentence is not grammatically correct. I think it should say "a million years ago" (with the article 'a').
In that case, it means 1,000,000 years before now.
But if you say 'millions of years ago' as in your second sentence, the meaning is not 1,000,000 years ago, but an undefined multiple of 1,000,000 years. It could be 3 million, or it could be 8 milion, or something else. But it's definitely more than 1 million, and probably more than 2 million.