The world champion, 29, set a time of 3 minutes 21.430 seconds in France on Sunday to continue an unbeaten streak in the competition going back to 2015.
Fellow Britons Tahnee Seagrave and Manon Carpenter, of Wales, were third and fifth respectively.
"I cannot believe it. It's been a mad weekend," said Wales-based Atherton.
"The track is so rough. Tahnee beat me in qualifying fair and square. I just thought 'this is it' and I've just got to out and do what I normally do.
"It's been two years of intense pressure but at the end of the day I love racing, it's such a buzz."
Britain's Rachel Atherton extended her record winning run to 14 with victory in the opening round of the 2017 UCI Downhill Mountain Bike World Cup.