The 83-year-old scientist, who lives in Edinburgh, insisted the reference was not funny and was actually misleading.
He came up with the theory of a subatomic particle, since dubbed the Higgs boson, which would explain the mystery of how things have mass.
But the professor wants people to stop referring to it as the "God particle" because he does not believe the particle holding the physical fabric of the universe together is the work of one almighty creator.
According to Prof Higgs, the nickname actually started as a joke, adding that it was "not a very good one".
The phrase was created for a popular science book from 1993 by Leon Lederman, a Nobel Prize-winning physicist, and Dick Teresi, a science writer.
Lederman wrote in the book "God particle": "This boson is so central to the state of physics today, so crucial to our final understanding of the structure of matter, yet so elusive, that I have given it a nickname: the God particle.
"Why God particle? The publisher wouldn't let us call it the Goddamn particle, though that might be a more appropriate title, given its villainous nature and the expense it is causing."
But Prof Higgs, explained his distaste for the term in a BBC Scotland interview. He said: "First of all, I'm an atheist.