The 51 year old was named as manager of the Southport at the end of last year after the depature of Alan Wright and has guided the club to safety.
A Club statement said Coleman had told them that he wanted to return to management in the Football League.
The former Accrington and Rochdale manager's assistant, Jimmy Bell, has also left the club.
The former Southport front man Coleman took over from Wright with the club in 18th place, having suffered six defeats in a row, and ensured their survival in the Conference Premier for a fourth successive year.
The Sandgrounders won eight, drew eight and lost nine of Coleman's 25 matches in charge.
The decision to part ways was taken following a meeting with club chairman Charles Clapham on Tuesday.