Chelsea have now scored eight goals in four days against Gary Megson's team, and were brutally destructive when confronted with a team a man down.
It was hard enough for Bolton when they had 11 on the park, but they were just victims for Chelsea to bully after Samuel's red card.
Frank Lampard's penalty in first-half injury-time set up this win, with the key moment being Samuel's red card for the trip on Didier Drogba which conceded the spot-kick.
Bolton worked feverishly but it was always a losing battle. Deco added the second and Zat Knight's own goal made it 3-0, before Didier Drogba grabbed a fourth in injury-time.
Bolton brought back goalkeeper Jussi Jaaskelainen and striker Kevin Davies, both rested when these two sides clashed in the Carling Cup fourth round at Stamford Bridge in midweek.
The hosts had Chris Basham in for his first start of the season as Bolton aimed to inflict Chelsea's third successive away defeat on them, while Chelsea reverted mainly to their Saturday-best side.
Tamir Cohen's header over from Lee Chung-Yong's free-kick was Bolton's only serious early chance as Chelsea had five decent early openings.
Drogba headed just over from a Nicolas Anelka cross, then 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.
Bolton persisted with their set-plays and aerial attacks aimed at Davies and Johan Elmander, and the ploy concerned Chelsea's defence.
The visitors had a 30th-minute Branislav 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.
Gary Megson made two half-time changes, sending on Ricardo Gardner and Paul Robinson for Basham and Lee.
Cohen lashed a free-kick over after John Terry had bodychecked Gardner in full flow, then Cohen was too slow to react to a fine Davies knockdown and Essien produced a remarkable saving tackle a yard out.
Drogba was booed every time he touched the ball by Bolton's fans, but he did not dive for the penalty having been clearly caught from behind.
Jaaskelainen made fine saves twice at the feat of the Ivory Coast star, and then from an Anelka effort before Lampard crossed an 18-yard effort against the bar.
Robinson was booked for a foul on Ivanovic before Jaaskelainen beat away a fierce Anelka drive after the former Bolton man had cruised past three defenders.
Chelsea had been under pressure in the air from set-plays, but when they broke from defence after 61 minutes they grabbed their second.
Anelka was the architect, streaming down the left before angling his pass for Deco to sidestep Paul Robinson's lunging tackle to clip the ball into the net.
Bolton sent on Mark Davies for Fabrice Muamba after 66 minutes, with Chelsea firmly in control.
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.
Bolton, to their credit, kept coming forward and won a succession of corners which Chelsea were at last beginning to defend properly.
But Chelsea got their fourth in injury-time when Anelka's cross was flicked on by Lampard for Drogba to fire home.