The 37-year-old Wilson, currently in his third season in charge at the Arms Park, turned down the offer of a contract extension and will move on next year.
“This was obviously a very difficult decision to make and I am very grateful to Cardiff Blues for the opportunities they have given to me,” said Wilson.
“I will be fully committed to Cardiff Blues for the remainder of my time here and am now solely focused on this weekend’s match with Munster.”
Cardiff Blues have confirmed that the search for a suitable successor will begin with immediate effect and further rugby appointments will be made.
“It is disappointing that Danny has decided not to take up the offer of a new contract and will not be part of our strategy moving forward. We will begin the process of finding a successor immediately and we will consult key individuals to ensure we make the right appointment for Cardiff Blues,” said Blues chief executive Richard Holland.
