The 45-year-old immediately assumes responsibility for all Academy operations with the club's outgoing Academy manager Dave Parnaby remaining to support two ongoing projects before retiring fully in March.
Liddle, a former Boro player who made 34 appearances during a four-year stay with the club between 1994 and 1998, was previously the club's Under-18s coach before stepping up to an interim head of coaching role within the Academy.
Boro CEO Neil Bausor said: "We're delighted to announce the appointment of Craig Liddle as our new Academy manager.
"Craig already knows the Academy well and how the club operates, and he will bring his own personality and ideas to what is a challenging role. His appointment ensures we will be able to continue and develop what is a vitally important area of our football club.
"I and everyone connected with MFC would like to wish Craig all the best for this exciting next step for himself and the Club."
Craig Liddle said: "I'm thrilled and honoured to be given this opportunity. I've enjoyed working closely with Dave for a number of years and have been able to learn from the knowledge and experience of one of the most respected Academy managers in the game.
"I know and understand the values of this football club and its Academy and I am looking forward to playing my part in the future and in the continued development of our young players."