Hosting City could have been three goals up within the opening five minutes. First Samir Nasri saw a shot blocked by David Wheater, then Mario Balotelli struck the post after collecting possession from Yaya Toure.
Balotelli had another chance moments later, but he sent Adam Johnson's low cross wide of goal.
The deadlock was finally broken by the home side in the 23rd minute. Full-back Gael Clichy struck an effort from distance which beat goalkeeper Adam Bogdan courtesy of a deflection off Wanderers defender Gretar Steinsson.
City continued to dominate after the restart, with Balotelli forcing Bogdan into low save in the 53rd minute.
Bogdan was beaten by his own teammate just before the hour mark, but thankfully for Bolton Darren Pratley's attempted clearance cannoned back off the crossbar before being cleared to safety.
Balotelli put the match beyond Bolton's reach in the 69th minute, flicking a cross from England international Johnson past Bogdan from close range.
Despite dominating for the remainder of the match, City were unable to extend their lead further.
City have now won 14 consecutive home games in the Premier League.