Morris joined the organisation back in 1997 at the end of his playing career with Glamorgan.
However, after 16 years in various different roles, the 49-year-old has opted to return to his former county, where he will shortly be announced as their chief executive and and director of cricket.
"This has been a remarkable period in the history of cricket in England and Wales and I have been extremely proud to having been able to play a part in it," he said in a statement.
"In my time at the ECB I have been fortunate to work with some extremely dedicated and talented cricketing people and I thank them and the board all for the support they have given me and their contribution to the success of the England teams.
"I am now looking forward to a new and exciting challenge with Glamorgan which I will tackle with energy, enthusiasm and relish. I wish the England teams at all levels and the ECB the very best of luck in the coming years and I am sure they will enjoy further success."
The ECB's chief executive, David Collier, went on to add that a replacement for Morris would be announced in the near future.