The 27-year-old beat the rest of the field by nearly 10 seconds to claim the 25th World Cup win of her career in Windham, USA.
Fellow Britons Manon Carpenter and Tahnee Seagrave finished second and third respectively.
"The World Cup overall means a lot because you have to be so consistent all year," Atherton said.
"World Champs you kind of let it go and it doesn't matter if you crash. The overall, week after week, the nerves, the worry - it is pretty intense so I am happy to finally have it back."
Atherton, a three-time world champion, regains the World Cup title she last won in 2013.
Her brother, Gee Atherton, finished fourth in the men's race, with the final round to take place on 22 August in Val di Sole, Italy.
Britain's Rachel Atherton sealed her fourth Mountain Bike World Cup downhill title with a fifth successive race win.