Abstract: The existing researches have already begun to pay attention to the negative externalities existing in the over-aggregation of regional enterprises. Compared with the“flocking together”in scale or form, more attention should be paid to the internal synergistic validity during the industrial agglomeration process. From the perspective of “geography, technology and organization”, this paper constructs the index of synergy effect of industrial agglomeration with the triple helix algorithm and finds out the characteristic facts that the synergy effect of industrial agglomeration in China is declining. The empirical results show that improving the synergy effect of industrial agglomeration can promote enterprise innovation and the promotion of enterprise innovation is mainly realized through resource allocation effect and knowledge spillover effect; the synergy effect of agglomeration has a greater impact on the innovations of private enterprises, the enterprises located in central regions, labor-intensive enterprises and start-up enterprises; poor market institutional environment and excessive government intervention will weaken the effect of industrial agglomeration synergy on corporate innovation. Therefore, local governments should develop effective industrial strategies and plans based on local geographical and resource advantages, and guide the introduction of enterprises and resources with the industrial chain as the center. The local governments should also strengthen the institutional construction, make the market play a decisive role in factor flowing and enterprise location selection, and let the enterprises become the core of industrial agglomeration and innovation.

Key words: industrial agglomeration; synergy; triple helix