Based on the data of 59 prefecture-level cities in the Yellow River Basin from 2011 to 2019, this paper uses the Slack Based Measure-Global Malmquist Luenberger (SBM-GML) model to measure green total factor productivity (GTFP) of the cities. Under the space–time concept of the Basin, heterogeneity analysis of the upper, middle and lower reaches of the Yellow River Basin is conducted. On this basis, a panel Tobit model is constructed to analyze the impact of environmental regulation on GTFP in the whole basin, upstream region, middle region and downstream region. The results show that the intensity of environmental regulation in the Yellow River Basin increases gradually, which is the highest in the lower reaches, followed by the middle reaches; spatially, the intensity of environmental regulation shows a certain aggregation trend. The green economic growth is realized in the whole basin, and the green technology progress effect is the driving factor of GTFP. The GTFP distribution in the upstream region is relatively concentrated, showing a slow upward trend. The distribution of GTFP in the middle reaches is discrete, and the annual difference is large. In the downstream region, it shows a trend of decline first and then increase. Environmental regulation promotes GTFP in the whole basin, upper, middle and lower reaches, accompanied by certain spatial differences. The Yellow River Basin breaks through the cost effect brought by environmental regulation and triggers technological innovation, thereby enhancing GTFP; the “Porter hypothesis” has been verified in the Yellow River Basin.