The co-agglomeration and integrated development of industries has become an important means for innovative development. This paper measures the degree of co-agglomeration between manufacturing and service industries and the quality level of urban patents, and empirically tests the urban patent quality improvement effect brought by the co-agglomeration and its internal influence mechanism. The results show that: the co-agglomeration of manufacturing and productive service industries can improve the level of urban patent quality. Therefore, the collaborative agglomeration of industries is a spatial prerequisite for enhancing regional innovation capabilities. At the same time, the discussion of the main impact mechanisms shows that knowledge spillover and deepening of division of labor are the main intermediary channels leading to the improvement of the urban patent quality. However, the intermediary promotion mechanism for accelerating the transformation of innovation achievements is still unclear. In terms of different regions, compared with underdeveloped regions, the co-agglomeration of industries in developed regions has promoted the improvement of the quality of urban patents more significantly; in terms of different industries, the improvement brought by the coordination of manufacturing and financial industry, scientific research and integrated technical service industry, water conservancy environment and public facilities management industry is even more obvious. Consequently, the problem of inadequate and unbalanced development of the co-agglomeration of manufacturing and productive services in China as a whole is the main obstacle to the improvement of urban patents quality.