It is well-known that regional innovation capability has become a decisive factor in establishing comprehensive competitiveness and gaining international competitive advantage for an area. A lot of existing researches suggest that spatial agglomeration could improve the innovation activities. For example, it makes the flow of knowledge and information more convenient. Using the innovation activities of 30 provinces and cities in 2009-2013 as a sample and from the perspective of industrial agglomeration, this paper measures the innovation efficiency of Chinese provinces and cities through super-efficiency meta-frontier function. Making use of exploratory spatial data analysis, this paper also emphasizes on exploring the influence of Marshall externalities, Jacobs externalities and Porter externalities on innovation efficiency. 

The empirical results can be concluded as follows: (1) Agglomeration externality is an important factor for innovation efficiency. The difference between the economic development stage of the eastern, western and central regions leads to the different effect of agglomeration externality on the innovation efficiency. The eastern region benefits from Marshall externalities, Jacobs externalities and Porter externalities, but the central and western regions benefit only from Marshall externalities and Porter externalities. (2) The spatial spillover effects ignored in previous studies has important influence on the innovation efficiency. And the provinces and cities within the same group show the tendency of “Club Convergence”, considering that the groups are more similar in industrial structure and resource endowment.

Based on the above research conclusions, this paper proposes the following policy recommendations: (1) Strengthen the linkage effect among different provinces/cities. Considering the spatial spillover effect of innovation efficiency in empirical outcomes, provinces/cities should strengthen cooperation with each other in innovation activities, and actively facilitate the exchange and sharing of technical knowledge among colleges, scientific research institutions and enterprises, creating a favorable knowledge spillover environment. (2) Speed up the construction of domestic market integration. Since the efficiency of innovation in the eastern, central and western regions all benefit from Porter externalities, the central government should break those segmented markets that develop at the expense of one another. It should encourage market competition, and promote the free flow of production factors such as talents among different regions. (3) The formulation and implementation of industrial plans should be based on the actual development level of the local economy. Local governments in many economically underdeveloped areas often emphasize one-sidedly the construction of complete industrial chains in the planning of related industries, hoping to rely on local superior industries to gather related upstream and downstream industries. Facts have proved that this kind of artificially created diversified industrial environment cannot promote the economic development of a province if its current development fails to reach a certain "threshold". Therefore, provinces/cities should formulate and implement industrial development plans based on local economic development and existing industrial foundations.