The Team Colombia- High Road rider won yesterday's 219km stage from Zottegem to Oostduinkerke in blustery conditions with a sprint that saw him finish ahead of Robbie McEwan.
Today, he took the 112km Stage 3a around the coastal town of De Panne again beating McEwan in a sprint.
"I did it last year, I thought I could do the double again this year," said Cavendish to www.cyclingnews.com. "Robbie was coming off my wheel, it was closer than yesterday."
Liquigas rider Frederik Willems led the way going into this afternoon's time trial which was won by Bradley Wiggins.