Assistant boss Dean Smith has also left the O's who have failed to win any of their last eight matches in all competitions.
Ling had been the sixth longest-serving manager in England, having taken charge of the club in September 2003.
He lifted the club from the depths of League Two to promotion at the end of the 2005-06 campaign, but the club are currently in the bottom four after losing 13 of their 25 League One games so far this term.
Youth team manager Kevin Nugent has been named caretaker boss, with goalkeeping coach Kevin Dearden working as his assistant.
The club hope to confirm Ling's full-time successor before the end of the month.