The level of science and technology governance of a city is directly related to the city’s ability to innovate. This report constructs the Evaluation Index System of urban innovation management and evaluates 36 key cities. According to the evaluation results，the overall level of innovation management of 36 cities has increased steadily in the past four years，while the sub-level is unbalanced，and the comparative changes of different regions are not obvious. Finally，in view of the present situation of urban innovation management，the author puts forward some pertinent suggestions from the aspects of innovation subject，high-tech，public service，innovation system and innovation environment. In particular，we should learn from the experience of Beijing，the development of new R & D institutions.