Abstract: Innovation factor agglomeration is a key way to integrate scientific and technological innovation resources, and an important way to promote new productivity through exploratory innovation and exploitative innovation. At present, the development of new productivity in China is facing challenges such as insufficient driving force of scientific and technological innovation, limited breakthrough of key technologies, and difficulty in obtaining innovative resources in underdeveloped areas. The agglomeration of innovative factors promotes the development of new productivity by breaking the limitations of traditional innovation models. However, there is still insufficient research on the systematic mechanism of innovation factor agglomeration affecting new productivity. In particular, the synergy of innovation factor agglomeration through ambidextrous innovation is still in the “black box”. How does innovation factor agglomeration affect new productivity through ambidextrous innovation mechanism? The existing research mainly discusses the agglomeration of innovation factors from the aspects of spatial distribution characteristics, influencing factors and economic effects, but there are few explorations on the different paths that affect the new productivity. Some scholars have made preliminary explorations on talent agglomeration, capital agglomeration and technology agglomeration as important research dimensions, but these studies focus more on the spatial distribution characteristics and agglomeration effect measurement of innovation elements. From the perspective of ambidextrous innovation, based on the data of 30 provinces in China from 2014 to 2023, this paper systematically explores the influence mechanism of innovation factor agglomeration on new quality productivity around the four action paths formed by the cross combination of two dimensions of network effect and scale effect and ambidextrous innovation. The results show that the agglomeration of innovation factors has a significant role in promoting new productivity, among which the positive effects of innovation technology and platform agglomeration are the most significant. As an important moderating variable, regional innovation environment significantly strengthens the positive impact of innovation factor agglomeration on new productivity. The agglomeration of innovation elements affects new quality productivity through the ambidextrous innovation mechanism. Although the short-term network effect of exploratory innovation is negative, it significantly promotes new quality productivity after scale, and can be transformed into exploitative innovation to form a continuous driving force. Further analysis from the factor dimension shows that among the four elements of innovative talents, capital, technology and platform, only innovative technology agglomeration and platform agglomeration have a significant positive impact on new productivity through the scale effect of ambidextrous innovation. The former enhances the technological breakthrough ability of innovation subjects by promoting technology spillover and knowledge diffusion, while the latter reduces innovation barriers and enlarges synergy effects as an important hub for the integration of innovative resources. Although talent agglomeration and capital agglomeration also show a positive relationship in some stages, their separate impact on new quality productivity is relatively limited, and they may need to be combined with technological innovation and platform construction to give full play to their effectiveness. This shows that in the current development stage, technological innovation and platform construction may be the core bridge connecting innovation elements and new quality productivity. The heterogeneity test also finds that the effect of innovation factor agglomeration is more significant in regions with higher levels of marketization, digital economy and transportation infrastructure. The marginal contribution of this paper is that, first, it reveals the mechanism of innovation factor agglomeration on new productivity from the perspective of dual innovation, and enriches the theoretical research on the formation mechanism of new productivity. Secondly, the two dimensions of network effect and scale effect are combined with ambidextrous innovation to form four action paths, and the system mechanism of factor agglomeration to empower new quality productivity is constructed. The third is to introduce adjustment effect and heterogeneity analysis to provide empirical basis for differentiated policies. The research conclusions provide theoretical basis and policy enlightenment for optimizing the spatial layout of innovation elements, improving regional innovation efficiency and promoting the formation of new quality productivity.