The paper constructed evaluation index systems of technology innovation capability for large-middle industrial enterprises, the regional technology introduction capability and regional science and technology input-output capability. By using multiple cluster analysis, we carried out the classification in three-dimensional and difference analysis of the regional innovation capability in China, and the results showed that there is significant geographical non-balance in the regional innovation capability of China. Finally, based on the results of empirical analysis, we gave the policy proposals to enhance the regional innovation capability of China.