Innovative manpower agglomeration and innovative capital agglomeration provide vitality and guarantees for a country to achieve high-quality development, and the improvement of the government's environmental governance capacity can guarantee the smooth advancement of the country's ecological civilization construction work; thus, it is very important to study the impact of innovation factor agglomeration on the government's environmental governance capacity. Based on this, this article establishes a mediated moderating effect model and a spatial econometric model, adopts the panel data of 30 provinces in China from 2009 to 2020 as an example, and divides innovation factor agglomeration into innovation manpower agglomeration and innovation capital agglomeration to study the relationship between them and the government's environmental governance capacity. The results of the empirical analysis show that (1) both innovation manpower agglomeration and innovation capital agglomeration can significantly promote the improvement of the government's environmental governance capacity. (2) Technological innovation plays a mediating role in promoting the government's environmental governance capacity through innovation factor agglomeration. Voluntary environmental regulation can promote the government's environmental governance capacity, but it attenuates the role of innovation capital agglomeration in promoting the government's environmental governance capacity. (3) Local innovative manpower agglomeration has a significant spillover effect, and innovative manpower agglomeration in neighboring places inhibits the enhancement of local governments’ environmental governance capacity. (4) Innovation capital agglomeration in neighboring places will inhibit the local government's environmental governance capacity, but its effect is much smaller than the promotion effect of local innovation capital agglomeration on the government's environmental governance capacity.