Flynn, who in mid-January was given a contract until the end of the season following Dean Saunders' move to Wolves earlier that month, has worked alongside Williams in the past.
Williams was Flynn's assistant during his time in charge of the Welsh youth set up and Flynn's number two when he was appointed caretaker manager of the senior Wales side.
"I have worked closely with David for a long time," said Flynn.
"We go back a long way and we complement each other. David has vast experience and knowledge and his coaching techniques are quality."
Williams most notably played for Bristol Rovers between 1975 and 1985 before finishing his career at Norwich, where he became assistant manager in 1988.
Similar roles at Bournemouth and Everton followed before Williams was appointed reserve-team manager at Leeds.
After completing a coaching role with the Manchester United youth set up in 2002, Williams returned to Norwich as assistant manager of the Canaries' academy. It was back at Carrow Road that he assisted Flynn in the Welsh set up.