The 50-year-old managed Orient between 2003 and 2009 but had been out of football since stepping down as Swindon Town boss in 2015 for health reasons.
On Thursday, a consortium led by Nigel Travis completed its takeover.
"His immediate goals are to develop the squad for next season and appoint a first-team coach," said Travis.
"His deep ties to the club will help him build on Leyton Orient's heritage of developing strong young talent through its academy."
After retiring from playing, Ling returned to the O's as a youth coach before moving up to the first team and winning promotion to League One in 2006.
Ling left Orient in January 2009 before spells at Cambridge United and Torquay United.
He moves to East London after Baskin Robbins and Dunkin' Donuts chief executive Travis purchased the club from Francesco Becchetti.
Orient were relegated to the National League at the end of last season, their second relegation in the three years under Becchetti, ending their 112-year stay in the Football League.
