Cox will be no.2 to Neal Ardley, who was confirmed as boss of the League Two strugglers on Wednesday afternoon.
The London club sacked boss Terry Brown in September after a poor run of League Two results, and have turned to a man who made almost 250 appearances for Wimbledon between 1991 and 2002.
More recently he has been academy manager at the Championship side Cardiff City, something which Dons chief executive Erik Samuelson said was key.
"Neal's background in bringing through young players fits perfectly with our commitment to youth development. We are looking forward to working with him," he said.
"We put the candidates through a very exacting interview process. They were all very impressive but it wasn't difficult to pick out the outstanding candidate for the role."
Cox retired from professional football in 2008, last playing for Crewe Alexandra. He had a short spell as manager of Leek Town during the 2010-11 season.
His first game alongside Ardley in the dugout at Kingsmeadow will be against Cheltenham on Saturday.