Which kind of city is more conducive to innovation has always been the focus of the scholars and policy-makers. Based on literature review, the theoretical hypothesis of the relationship between city administrative level and enterprise innovation were put forward. Second, based on survey data of Chinese industrial enterprises and city statistics, the influence of city administrative level on enterprise innovation was empirically tested. The results show that, the level of administrative division in the location of enterprises significantly promotes enterprise innovation, on average，the output value of new products of enterprises located in municipal districts is about 29.67% and 34.37% higher than that of enterprises located in county districts and townships, respectively. The innovation effect of city administrative level is also very significant, which is enhanced with the promotion of city level. In addition, resource allocation capacity and agglomeration effect may be important channels for high-level cities to promote enterprise innovation.