This paper empirically investigates the unbalanced and inadequate development of regional innovation in China from the view of national central city by comprehensively using statistical analysis, DEA model and spatial econometrics. According to the result: the national central cities rank the top among most innovative activities, and have significant advantages over their surrounds. Beijing, Chongqing, Chengdu and Xi 'an in recent years have reached a relatively optimal efficiency of innovation, but Shanghai, Guangzhou Tianjin, Wuhan and Zhengzhou suffer from an inadequate development of innovation due to their excessive talents and weak transformation of scientific and technological achievements. The majority of national central cities positively lead a collaborative innovation of their surrounds except Xi 'an. Accordingly, the national central cities are divided into mature ones (Beijing, Shanghai, Guangzhou), growing ones (Xi 'an, Wuhan, Chengdu, Zhengzhou) and dual-core complementary ones (Tianjin and Chongqing).