Innovative industrial clusters are is an important platforms carrier to for cultivatinge new industries and promotinge regional innovation. Data Envelopment Analysis (DEA) is used to analyze the innovation efficiency of 109 innovative industrial clusters in China. The results show that the overall comprehensive efficiency of innovative industrial clusters in China is low, and only one tenth of the total efficiency of innovative industrial clusters is effective for DEA operation. There are obvious regional differences in innovation efficiency of innovative industrial clusters amongacross provinces and regions, and the overall distribution trend is "high in the East and low in the west". For innovative industrial clusters with ineffective DEA, the total number of enterprises, innovative service institutions and tax payment have a significant impact on innovation efficiency. It is suggested that appropriate measures should be taken to improve the innovation efficiency of China's innovative industrial clusters by adjusting the proportion of resource allocation, building constructing the resource sharing mechanism, of resource sharing and optimizing the innovative service models.