Aquatic products are important sources of protein and food consumption, which are pivotal to solving the problem of food shortage. As the world’s largest producer of aquatic products, China’s aquaculture has developed rapidly. However, a large quantity of pollutants has also been generated in the fish farming process, which is detrimental to the sustainable development of China’s aquaculture. Therefore, under double constraints with regard to resources and the environment, fishery development must achieve cleaner production. Measuring green total factor productivity in aquaculture is fundamental to improving aquaculture production efficiency and reducing pollution emissions. This paper investigated the green total factor productivity in China using the SBM-ML method and analyzed the dynamic evolution of fish farming, measuring its change characteristics with regard to time and spatial differences. The results indicated that the total factor productivity indexes of mariculture and freshwater aquaculture in China are 1.050 and 1.060, respectively. Regionally, mariculture in the East China Sea region has the highest green total factor productivity of 1.072, followed by the South China Sea region with 1.056, and the green total factor productivity in the Yellow Sea region is the lowest—only 1.030. The results of the freshwater aquaculture calculations showed the opposite geographical distribution characteristics in China, with the highest in the western region (1.098), followed by the central region (1.046), with the lowest being in the eastern region (1.038). Evidently, both mariculture and freshwater aquaculture have noticeable spatiotemporal heterogeneity. Relevant policy recommendations are provided to improve the green production efficiency of fishery.