The relationship between environmental regulation and green total factor productivity has always been a hot topic in academic circles. However, few studies have focused on how economic environmental regulation affects green total factor productivity in the Yellow River Basin. Taking nine provinces and ten demonstration cities in the Yellow River Basin as samples, this paper uses the fixed panel model to explore the direct, indirect and threshold effects of investment type and cost type environmental regulation tools on green total factor production. The results are as follows. There is a U-shaped relationship between investment type and cost type environmental regulation and green total factor productivity. Investment type and cost type environmental regulation can promote green total factor productivity indirectly by forcing the evolution of pollution structure. By forcing the evolution of pollution structure, the indirect impact of the two types of environmental regulation on green total factor productivity has a threshold effect, and the U-shaped relationship inflection point of investment regulation reaches earlier than that of cost regulation. It is suggested that the government should know the function principle of each economic environmental regulation means when formulating environmental regulation policies, give full play to its incentive role, and adopt appropriate strategies according to local conditions in view of the heterogeneous pollution industrial structure in various regions, so as to fundamentally improve the green total factor production rate.