Under the background of accelerating scientific and technological progress and continuous expansion of technology scale in China, the policy of national independent innovation demonstration zones has been continuously deepened and improved, which promotes the development, transformation and upgrading of innovative economy in China and provides important support for the construction of regional innovation system. Based on the panel data of 285 cities in China from 2003 to 2020, this paper uses the difference in differences (DID) method to explore the impact of the national innovation Demonstration zone policy on regional innovation Capability, and to analyze and test the mechanism of diversified agglomeration and specialized agglomeration of hightech service industries in the relationship between the two. Further, this paper tests the heterogeneity of policy effect in regions and policy layout; The spatial econometric method is introduced to consider the spatial spillover effect, and the spatial Durbin model is used to further explore the impact of the policy of the national Independent Innovation Demonstration Zone on regional innovation. The empirical results show that the establishment of the national Independent Innovation Demonstration Zone can promote regional innovation capability; The agglomeration of high-tech service industry plays a mediating role in the relationship between the two. The impact of the policy on innovation in the western region is much stronger than that in the eastern and central regions. Through the comparison of policy pattern, the policy effect of the single-city layout is much higher than that of the multi-city layout; There are significant negative externalities in the impact of the national independent innovation demonstration zone policy on regional innovation capability.