Jones played a leading role in Scotland's entry into the one-day cricket National League last summer.
"Without Gwynne, the profile of Scottish cricket would not have been raised to its current level," said Cricket Scotland chairman Keith Oliver.
"Gwynne told me he feels he has completed his main objectives. These were to promote the game using his international contacts and influence, to professionalise the management with a high calibre executive team and to set the vision and prepare the way for Scotland to become a full one-day international nation in the medium term and a Test-playing nation in the long term."
Gwynne Jones has parted company with Scottish cricket after two years as its chief executive.
