Abstract:This paper constructs a theoretical regional innovation system, based on the perspective of industrial knowledge bases and the regional division of headquarters economy center cities. Industry knowledge bases play the role of innovation resources, institution works as external factor, headquarters economy characteristic is the internal endowment, and all of them comprehensive influence innovation configuration and further influence the construction type of the regional innovation system. The regional innovation system of forward support type, backward support type and network support type are constructed in this paper, in which the thorough analysis and proper countermeasures are proposed for regional innovation systems construction in Chengdu, Shanghai and Beijing as the typical headquarters economy center cities.