The White House said Philip Cooney's sudden departure was totally unrelated to the allegations.
He was chief of staff at the White House Council on Environmental Quality.
Critics say his alterations cast doubt on the link between greenhouse gas emissions and climate change, accepted by most scientists.
"[Mr Cooney] had accumulated many weeks on leave, and so he decided to resign and take the summer off to spend some time with his family," presidential spokeswoman Erin Healy told AFP news agency.
By the way, it's not just "critics" who say his edits downplayed the link between greenhouse gases and climate change. Everyone agrees on the nature of the edits. It's just that "critics" are the only ones who care.