Abstract: Green development is important for China’s future food safety, and measuring green productivity is an effective method to explore ways to increase green grains production. Based on the differences in the endowment of cultivated land resources in different regions, this study adopted the ecological services value evaluation method to measure the ecological value of cultivated land during the process of grain production. To incorporate the nutrient pollution and non-nutrient pollution generated in the process of grain production, the global Malmquise Luenberger index and the super efficiency model were used from the static and dynamic perspectives, to calculate China’s total factor productivity and input-output redundancy rate from 1997 to 2019. To better understand the temporal and spatial changes in China’s green total factor productivity, the spatial development characteristics of the agricultural production factors were investigated in the selected six years (1997, 2001, 2005, 2009, 2013 and 2019) using the equidistant distribution method, and Moran’s I index was used to study the spatial heterogeneity and agglomeration of green total factor productivity of grains in China. The results showed that: 1) During the study period, the ecological value of grain production reduced by 0.39%, from 647.157 billion Yuan in 1997 to 644.616 billion Yuan in 2019; a loss of 2.541 billion Yuan. The ecological value in the northeast, central, and southwest regions increased, whereas that in the east and northwest regions decreased. 2) Analysis of the environmental impact of grain production showed that the traditional total factor productivity, which does not consider environmental effects, tended to ignore the positive and negative aspects of grain production and cannot accurately assess the true efficiency of China’s grain production. After accounting for environmental factors, such as the ecological value of grain production and agricultural non-point source pollution, this study found that the green total factor productivity of grains increased by 0.60% annually, from 0.9754 in 1997 to 1.0990 in 2019, driven mainly by technological progress (1.0308). The driving effect of technical efficiency (0.9973) was weak. 3) The proportion of provinces (cities) that were relatively effective in the green total factor productivity of grains increased from 9.68% in 1997 to 67.74% in 2019. In terms of time and space, the relatively effective provinces (cities) was mainly in the eastern region and then graduallydeveloped to the northeast, central, and northwest regions. 4) Due to high pollution emissions and resource consumption, the main reasons for the provinces (cities) that were relatively ineffective in green total factor productivity of grains were the redundancy of employees in the primary industry, the use of agricultural film, and carbon emissions. 5) The green total factor productivity of grains in China had a significant positive spatial correlation dominated by high-high agglomeration, and the green total factor productivity of grains showed spatial characteristics of agglomeration in the central and southwestern high-efficiency areas. The degree of agglomeration was increasing. Based on the above results, this study advocates for a better understanding of the positive and negative effects of grain production activities, strict control of the non-grain and non-agricultural phenomenon of agricultural land, and the promotion of advanced agricultural technologies to promote the green total factor productivity of grains.