Healthy city is an important part of social governance. Improving the level of social governance can provide the favorable environment for building the healthy city. This paper starts with the definition of the concept of institutional innovation of social governance，and then describes the main results of the innovation in the few years，combining with the vivid practice of social governance in Beijing：in the social governance system increasingly sound，grassroots social governance innovation is gratifying.This paper holds the principle of problem orientation，draws on the foreign experiences，and puts forward practical suggestions for institutional innovation of social governance in Beijing：We should improve the multi-faceted social governance system led by the Party and the government，strive to straighten out the grass-roots social governance mechanism，actively promote the construction of a society ruled by law，consciously stimulate the social governance function of cultural education，and make full use of information technology to enhance comprehensive governance capacity.