Orient took the lead when Shaun Batt scored from the spot and he grabbed his second a minute before the break.
He slotted home a third before the hour and although Bradley Dack headed in a consolation for the hosts, Orient continued their impressive start to the season.
The League One leaders were on the back foot initially but they took the lead after Cody McDonald tripped Romain Vincelot in the box and Batt dispatched the resulting penalty with ease.
In the final minute of the half Orient doubled their lead when Batt volleyed home Moses Odubajo's cross from close range.
Just before the hour mark Batt completed his hat-trick after finishing a storming run into the box by rolling the ball past Stuart Nelson.
Dack pulled one back with a header when Orient failed to deal with a long throw but it was merely a consolation.