Jim Gannon stuck by the eleven that started Friday's FA Cup-tie against Wycombe Wanderers.
Loanees Keith Treacy and Tony Kane, unable to play against the Chairboys were back on the bench alongside Adam Griffin who missed Friday's game through illness.
The Dons, knocked out of the FA Cup by Blackpool on Saturday, included former County striker Aaron Wilbraham.
Dons kicked off with a powerful wind at their backs and soon put the County defence under pressure.
Keith Briggs had to come to the Hatters rescue with a timely intervention on 5 minutes to block Lloyd Dyer who had burst into the box unchallenged.
A minute later Izale McLeod fired over from 25 yards.
A miskick from Rob Clare on 14 minutes presented Dyer with another chance that Ashley Williams did well to block.
Although under pressure the County defence was protecting James Spencer well but, on 19 minutes, the 'keeper had to make his first save when he turned away a shot from the lively Dyer.
Wilbraham then came close with a cushioned volley from Paul Butler's flick fortunately the ball bounced just wide.
Adam Proudlock, who has just agreed a new contract at Edgeley Park, made ground down the right and pulled the ball back to the penalty spot. Jason Taylor and Stephen Gleeson both had half chances before the ball was cleared.
Gleeson then fed Michael Rose on the left and the fullback hit a terrific low cross that Dean Lewington sliced just wide of his own post.
From the resultant corner Taylor saw his near-post flick saved by Lee Harper.
Five minutes before the break Wilbraham came close to scoring against his old club with a low drive from the edge of the box that flew just wide.
The half closed when Dyer cut inside from the right and hit a curling drive just over.
Half time: M K Dons 0 County 0
The first chance after the break came from McGovern's corner but Wilbraham couldn't direct his header on target.
County responded when Proudlock turned and shot in one movement but Harper made the save.
Dons took the lead on the hour when Keith Andrews lofted the ball towards the far post. Williams miscued a header to McLeod who beat Spencer with a brilliant scissor kick.
The Hatters almost levelled from the next attack. Briggs crossed from the right but Bramble was off target at the near post.
Disaster struck on 68 minutes when Williams was adjudged to have brought down McLeod when through on goal. The referee red-carded the County defender and awarded a penalty.
After consulting his assistant the match official changed his mid and gave Dons a free kick on the edge of the box that Dyer fired over.
Dons wrapped things up on 74 minutes when Dyer out-muscled Rose down the right and crossed to McLeod who superbly lofted the ball over Spencer.
And things went from bad to worse for the Hatters in the dying moments when Rob Clare was dismissed for a second yellow card, allegedly for hand-ball.
Red Cards
County: Williams 68, Clare 90 (2 yellows)
Yellow Cards
MK Dons: O'Hanlon
County: Bramble, Gleeson, Taylor
