Abstract:This paper selects R D and patent output data of Beijing, Shanghai, Tianjin, Chongqing, Shenzhen, Qingdao, Chengdu, Wuhan, Hangzhou in total nine cities from 2008 to 2015. On the basis of fully demonstrated correlation, the composite index system is composed by four indicators, which are “The number of invention patent applications generated by R D expenses”, “The number of invention patent applications generated by Full-time Equivalent of R D Personnel”, “Invention patent grants generated by R D expenses”, “Invention patent grants generated by full-time equivalent of R D personnel”. Then the paper comprehensively analyzes the output efficiency of the sample cities’ innovation input, and tries to explore the characteristics and rules of the sample cities’ innovation efficiency through vertical and regional comparative analysis.