Abstract:Accelerating process of economic globalization makes the world a new division of labor based more on regional rather than according to the state,in order to evaluate the regional innovation performance more scientific and reasonable ,this paper based on two-stage dynamic DEA model,using DEAP2.1 software to evaluate the innovation performance of Beijing、Tianjin、Shanghai、Chongqing、Guangzhou、Shenzhen and other 11 cities from the R D input and the commercialization of scientific and technological achievements in two stages. The results show that: (1)Whether in the first stage of the innovation performance or the second phase of the innovation performance, Harbin both reached the technology and scale of effective effectively;(2)The technology and scale of Shanghai、Harbin and Hangzhou in the first stage is effective,the pure technical efficiency of Chongqing and Xian is effective;(3) The technology and scale of Tianjin、Guangzhou、Shenzhen、Harbin、Qingdao in the second phase is effective.