The 14th five year plan proposes to build a number of regional innovation highlands with international competitiveness. It is an important work content for each city science and technology management department to build a scientific and technological service platform and improve the innovation ability of enterprises during the 14th five year plan. This report constructs the evaluation index system of urban innovation management from five dimensions of innovation input，innovation potential，innovation carrier，innovation efficiency and innovation output. The evaluation and ranking of innovation management level of 36 key cities is carried out，which focuses on reflecting the overall situation of urban innovation management and innovation promotion in these cities. Finally，according to the key points of urban innovation management during the 14th five year plan，the paper puts forward some suggestions from the construction of smart city，the financial tools of science and technology，the mode of scientific research organization and the innovation of management system.