The 2016 Masters champion is 16 under after a third-round 67, three shots clear of American David Lipsky and four ahead of France's Alexander Levy.
However, Willett, 29, says a three-shot overnight lead may not be enough to secure victory in Kuala Lumpar.
"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.
"One or two under par is a good knock out there, and there's a few guys that can go low if it's windy."
England's Tommy Fleetwood and Lee Westwood are nine shots off the pace at the Saujana Golf and Country Club on seven under, with Scotland's Marc Warren - who had led after the first round - a shot further behind after a third-round 72.
England's Robert Rock and James Morrison are five under after shooting 73 and 74 respectively on Saturday.
England's Danny Willett leads by three shots going into the final round of the Maybank Championship on Sunday.