The 29-year-old carded a second consecutive 67 to add to his opening 66 and sits on 16-under par with just 18 holes to go at Saujana Golf and Country Club.
The Sheffield-born star managed six birdies and dropped one shot at the fifth, ending the day three strokes clear of American David Lipsky, who reached -13 after a four-under-par 68.
Frenchman Alexander Levy is a further shot back after a 67 while five players share fourth place on -11, including Austria's Bernd Wiesberger, who could only shoot a 73 compared to Friday's 63 and is now back in the chasing pack.
Gregory Havret and Panuphol Pittayarat are also on that mark and it will take a low score from anyone outside 11-under to take the title, but Willett admits he has no idea what the winning score will be.
"I'm not sure what will win it to be honest, it depends on if we pitch up and it's flat calm," he said. "I think there's a few guys that can go low if it's windy like this.
"One or two under par is a good knock out there so I think it all depends on the weather tomorrow."