Ling, who was the 6th longest serving manager in the Football League having been at the club since September 2003, has left the club by mutual consent after the O's 2-1 home defeat to Bristol Rovers on Saturday.
Orient have won just five league games all season and lost their last four.
Ling's departure, which also sees assistant boss Dean Smith leave Brisbane Road, comes at a time when the club sit 21st in League One.