The the Wikipedia page on "little Green men" is actually quite thorough. William S Burroughs wrote science fiction about green Martians, and that's likely where the notion really comes from.

Visually, the Flintstones in the 1960s popularized the image of a small green alien with a big head with The Great Gazoo. The big black eyes came later with the 1987 abduction book Communion and it's iconic cover.

For what it's worth, I have never come across a real report of a "little green man". There are plenty of reports of little men, with and without big heads and big black eyes. There are also plenty of reports of little grey men, and some of little hairy things with claws. But "little green men" seems to come entirely from pop culture, not from the reports of "abductions", "contactees", and "close encounters of the third kind". I assume there are some reports fitting that description out there somewhere simply because there are so many reports on record. But I've always thought that the conspicuous lack of reports of little green men shows that pop culture doesn't have that strong of an influence on what people say they see. Otherwise we'd expect more little green men running around in the abduction literature. Though I confess that's hardly an ironclad conclusion and is more of a hunch.