Abstract: The two-stage DEA model of sharing input was used and a multi-link innovative city evaluation index system was constructed to evaluate the innovation efficiency of innovation-oriented cities in the Yangtze River Delta region. The results are as follows:the relevant cities should consider not only technological innovation but also economic, social and ecological benefits in the process of the nation's construction of innovative cities in the future. In terms of capital investment, it is necessary to build a financial innovation system to deepen the construction of capital market, and to enhance the support of innovation and entrepreneurship to strengthen the capability of scientific and technological financial services. In the construction of innovative cities, the adjustment of the industrial structure should be quickened, the development of independent start-ups and innovative small and medium-sized enterprises should be encouraged, and the construction of urban ecological civilization should be accelerated.