The Blues dominated much of the play and went ahead in first-half injury time through a Frank Lampard penalty, Jlloyd Samuel being sent off for his trip on Didier Drogba.
Chelsea broke from defence after 61 minutes for former Bolton striker Nicolas Anelka to set up Deco for the second, with the third going in off a combination of Branislav Ivanovic and Wanderers defender Zat Knight before Drogba claimed the fourth.
Drogba headed just over from a Anelka cross, then Jussi Jaaskelainen touched over another effort from the big striker before saving from Anelka.
Michael Essien flashed an angled effort just wide, before Drogba got clear and was only halted by Jaaskelainen's outstretched boot.
The visitors had a 30th-minute Ivanovic strike ruled out by a linesman's flag - Michael Ballack was adjudged to be offside. Chelsea players complained bitterly, but referee Peter Walton was unmoved.
Bolton were soon back under pressure - and in the final seconds of injury-time, Chelsea were ahead, after Drogba had been brought down. Lampard lashed home the penalty.
Jaaskelainen made fine saves twice at the feat of Drogba and Lampard hit the bar from 18 yards, before , Deco doubled the lead in the 61st minute, receiving the ball from Anelka, sidestepping Paul Robinson's lunging tackle, then clipping the ball into the net.
Paulo Ferreira was booked late on, but Chelsea were in full control and it was 3-0 when Knight - under pressure from Ivanovic - got the final touch to Ricardo Carvalho's cross.
The home side, to their credit, kept looking for a goal but Chelsea got their fourth in injury-time when Anelka's cross was flicked on by Lampard for Drogba to fire home.