Based on the innovation elements of 19 key cities,the evaluation index system of urban innovation ecosystem is built, including five dimensions and twenty secondary indicators ,that is innovation environment, innovation payment, innovation kinetic energy, development trend and openness level.Principal components and calculate comprehensive scores are extracted with the method of global principal component analysis, in accordance with the index data from 2017 to 2019,and the urban innovation ecosystem is classified are put forwardby utilizing the method of hierarchical cluster analysis. The results show that innovation environment and innovation payment have significant effects on the urban innovation ecosystem. The urban innovation ecosystem have aroused more and more attention of of various cities, but the point difference expand.Significant difference is observed among the cities. Therefore, the following suggestions improving the quality of “hard innovation environment” and “soft innovation environment”，establishing and optimize the whole ecological innovation system，cultivating strong driving force, and accelerate the coordinated development of cross-regional innovation systems.