Deputy executive director John O'Brien is taking over until a permanent successor is appointed in the autumn.
Mr Usher said: 'Setting up IDeA from scratch has been immensely rewarding. We've recruited some of the most talented people in the business and I am proud of our achievements.'
Society of Local Authority Chief Executives & Senior Managers director general David Clark said: 'IDeA was a unique experiment to see if an industry can improve itself. Under Mel it has transformed itself - the experiment has been a success.'
Mr Usher rose to prominence after South Somerset DC, where he was chief executive, won Council of the Year in the first LGC Awards for Excellence 1997.
Serving chief executives were quick to praise his achievements. Lewisham LBC chief executive Barry Quirk said: 'His passion for innovation combined with a commitment to local government placed the agency at the heart of public service reform.'