Larnell Cole provided the crosses for both goals with Nick Powell and Federico Macheda making it six points out of six in the competition for the top-of-the-table Reds.
United took a little while to get the passing game going although Larnell Cole looked bright from the outset. Powell had the first effort but shot over the bar after a neat spin while Jesse Lingard also mustered an attempt on the turn that tested Lewis Fielding.
Bolton's clearest opening in the first half fell to Gregg Wylde, who found himself through on Sam Johnstone's goal but the keeper was out quickly to block the finish. The Reds regained control as Macheda's snap-shot again worked Fielding before the Italian striker rolled agonisingly wide from Lingard's perfect through pass.
That proved to be the closest the two sides came to a goal before the half-time whistle although Lingard did force Fielding to tip a stinging drive over the top when Powell escaped with what looked a clear foul in midfield.
Warren Joyce's side began the second half with much more purpose and should have broken through. Michael Keane's goalbound shot was blocked by Oscar Threlkeld and Powell's 30-yard scorcher was matched by Fielding's save. Somehow Wanderers survived a Tom Thorpe header and dangerous Powell centre and Lingard twice failed to finish, with the second opening coming after a brilliant run through the middle and a return pass from Cole.
Completely against the run of play, Ben Hampson rose to head a Wylde corner into the net to stun the home crowd and play became very scrappy after the goal with a couple of stoppages for