The relative price of factors determines the optimal production structure of enterprises. Population ageing leads to the decrease of effective labor supply and the increase of labor costs, and thus affects enterprise innovation. This paper links the city-level census data to the data of micro industrial enterprises and analyzes the impact of regional population ageing on enterprise innovation outputs. The results show that (i) the current low level of population ageing has significantly promoted the innovation of Chinese enterprises, while population ageing exceeding a certain inflection point in the long run will inhibit enterprise innovation; (ii) compared to other types of enterprises, population ageing is more likely to promote innovation in nonstateowned enterprises and capital-intensive enterprises; (iii) the ageing of Chinas population has promoted the innovation of enterprises in eastern and central regions, while it has negatively affected the enterprise innovation in western regions; (iv) population migration restrains the promotion effect of population ageing on enterprise innovation in eastern region. Policies should optimize the input of production factors, cultivate the quality demographic dividend, and promote the coordinated regional development of innovation.