Improving the regional innovation system and developing new organizational innovations to continuously enhance regional innovation capabilities are key measures for building a regional innovation hub and achieving high-quality economic development. This study first theoretically elucidates the impact mechanism of enterprise innovation agglomeration and government policy uncertainty on regional innovation capability, and thus clarifies such impact on regional organizational innovation. Based on urban panel data, this article empirically analyzes their impact on regional innovation. Based on the research results, the agglomeration of manufacturing industry in cities can significantly improve regional innovation capabilities. The policy uncertainty brought about by the mobility of municipal party secretaries has a restraining effect on the enhancement of regional innovation capabilities. The higher the degree of marketization in a city, the more significant the role of manufacturing agglomeration in enhancing regional innovation capabilities, thereby weakening the inhibitory effect of policies.