Abstract: Based on the five aspects of innovation resource, innovation investment, innovation output, innovation environment and innovation performance, a synthetic evaluation on the innovation capacity of Jiangsu Province and Anhui Province is made and the reasons for the differences of innovation ability between them are also analyzed. The results show that there is a big gap between Anhui Province and Jiangsu Province in terms of the number of innovative talents, the quality of enterprises, the integration of colleges and universities with industry and the intensity of government investment. On the whole, the innovation ability of Anhui Province is still insufficient, compared with that of Jiangsu Province. In order to improve regional innovation capacity, Anhui Province should attach importance to the cultivation of innovative talents, strengthen the dominant position of enterprises, give full play to the overall role of the government and cultivate the advantages of industrial development.