Innovation-driven development is China’s basic development strategy into a new era and the key to realizing the transformation of old growth drivers into new ones. Urban agglomeration has become the basic geographical unit for countries to participate in international competition. Therefore，it is of great theoretical and practical significance to enhance the innovation ability of urban agglomeration in China. This paper takes Beijing-Tianjin-Hebei，Yangtze River Delta，Pearl River Delta and Chengdu-Chongqing economic circle as the research object. Based on 2013-2018 data from the three dimensions of innovation input，innovation output and innovation environment，the entropy method is used to construct an evaluation index system for urban innovation capabilities，and to measure and analyze the innovation capabilities of urban agglomerations. The results show that：in terms of the comprehensive innovation ability，the comprehensive innovation ability of each urban agglomeration is at a high level，but the regional development of the comprehensive innovation ability is not balanced. In terms of the internal indexes of innovation ability，the overall indexes increase steadily，but the development structure of the internal indexes of innovation comprehensive ability is not balanced. Finally，three countermeasures and Suggestions are put forward on this basis. Increase investment in innovative resources and improve the efficiency of scientific and technological achievements transformation；Give full play to the functions of the government，optimize and improve the innovation environment of urban agglomeration；Strengthen innovation cooperation within urban agglomerations.