As an important part of agricultural new quality productivity, the improvement of grain green total factor productivity scientifically explores the grain green production effect of high-standard farmland construction, and provides reference for the development of agricultural new quality productivity and the transformation of grain green production. This paper analyzed the effect of high-standard farmland construction on grain GTFP and its mechanism by using panel data of 31 provinces (cities and districts). Different from the traditional non-parametric method, the stochastic frontier method, which can deal with measurement errors and noise problems, is adopted to measure the agricultural environmental pollution index as a negative factor into the model, so as to measure the current agricultural green development situation more accurately. SFA measurement shows that there is still room for improvement of green total factor productivity of grain in China. Theoretical and empirical analysis verify that high-standard farmland construction is one of the important measures to improve green total factor productivity of grain. Concretely speaking, every unit increase of high standard farmland construction level can increase the total factor productivity of grain green by 0.105 unit. This conclusion is still robust after replacing explained variables, core explanatory variables, considering endogenesis, sub-construction stages and supplementary sample data. Heterogeneity analysis shows that the impact of high-standard farmland construction on grain GTFP has significant heterogeneity at the level of agricultural production area positioning, economic development degree and production conditions. Among them, at the level of agricultural production area positioning, high-standard farmland construction has a better effect on improving grain green total factor productivity in main grain production areas, which should benefit from specialization and scale management in main grain production areas, thus promoting the adoption of more efficient and low-carbon agricultural green technologies. In addition, the political task of food security will also promote the construction effect of main grain-producing areas to be better than that of non-main grain-producing areas, which is more conducive to the improvement of GTFP in main grain-producing areas; At the level of agricultural production conditions, the construction effect in areas with better production conditions is better than that in areas with poor production conditions, because there is a better basis for the use of agricultural green technologies, which is more conducive to the popularization of new technologies, and better production conditions will also play a role in improving factor utilization efficiency and reducing factor input. The mechanism test shows that increasing farmland management scale, adjusting agricultural planting structure and improving agricultural factor quality are important ways to improve grain GTFP by high-standard farmland construction. The threshold effect shows that the green production effect of high-standard farmland construction in plain and mountainous areas before threshold is more obvious than that after threshold. Therefore, we should explore high-standard farmland construction models according to local conditions, promote moderate-scale operations and improve specialized grain production capabilities, thereby promoting the continuous rise of new agricultural productivity represented by green total factor productivity of grain.