In recent years, the increasingly serious challenges of climate change and environmental pollution problems have changed conventional economic growth pattern of the world. The new pattern is to effectively keep up with the premise of the original level of economic development while improving the environment, and making full use of the resources have become a hot topic of the whole society. The low-carbon economy provides a new way to solve this problem, which is expected to become the new engine of the world's economic development. To imply green innovation and develop green economy, the core is to improve resource utilization efficiency and reduce damage to the environment of economic growth. The key point lies in the improvement of low carbon green innovation ability and the increase of green innovation efficiency. By fully taking into consideration the gap in green innovation technology, this paper uses the undesirable output Meta-frontier function to estimate China's green innovation efficiency, and employs the structural equation model to study the mechanism of the key factors. The study shows that: (1) Due to significant differences in green innovation production technology among the three different regions, the green innovation efficiency presents a descending order of the pattern of East-West-Central; (2) Whether the East or Midwest China, fine industrial structure, free technology trading market and other infrastructure environment have a greater promoting function than other elements; (3) China's environmental regulation policy urgently need to change from mandatory to incentive-based policy in order to improve the enthusiasm of enterprises to implement cleaner production and improve green innovation efficiency of China. The above research has important theoretical and practical significance for the improvement of China's innovation ability under the background of building an innovation-oriented country. On the one hand, one should not only focus on the improvement of economic and social development level, but also pay attention to harmonious coexistence between human and nature, and imply low-carbon green innovation. On the other hand, by considering numerous differences among various regions in terms of technological innovation capability, one may argue that differentiated development policy should be made and carried out by the government according to the features of different districts, and the mechanism and the path of the related factors for green innovation. The government should encourage Midwestern regions to adjust industrial structure, increase the investment of cultivating innovative and entrepreneurial talents, and promote the incubation of high-tech industry. These measures can help transform compulsory environmental regulation policy into incentive oriented environmental regulation policy, and improve the enthusiasm of enterprises to implement cleaner production. The government should also intensify the cooperation of industry and research in the East and West regions in order to realize the coordinated development of Regional Green Innovation.