Saturday's 2-1 home defeat by Northampton brought the curtain down on a disappointing season for the seaside club, in stark contrast to their play-off finish in 2009/10.
McIlroy, who led Morecambe into the Football League after taking over in 2006, said: "I have had a fantastic time."
He added, on the club's official website: "I am delighted that I was able to lead the club into the Football League along with Mark Lillis and will always have great memories from my time there."
Elsewhere in League Two, Gillingham manager Andy Hessenthaler is hoping to stay in charge at Priestfield despite failing to guide his side into the play-offs while Paul Sturrock is confident that Southend United will finish higher up the table than 13th next season.
On the transfer front, Oxford United have released striker Jack Midson, defenders Djoumin Sangare and Mitchell Hanson and goalkeeper Simon Eastwood while Richard Walker, Richard Jackson, Keith Gilroy, Lewis Young and Garyn Preen are leaving Burton Albion.