Abstract: Environmental problems caused by increasing agricultural non-point source pollution and agricultural carbon emissions are one of the main challenges to sustainable agricultural development. Given the importance of grain production in agriculture, promoting low-carbon and green grain production is critical for coping with agricultural environmental threats. The Yangtze River Economic Belt is the core area of grain production in China; therefore, accurately measuring the ecological total factor productivity of grain in the Yangtze River Economic Belt and systematically analyzing its temporal and spatial evolution characteristics can provide a data basis for promoting the sustainable development of agriculture in this region and realizing the goal of protecting the Yangtze River. Based on the grain production data of 110 prefecture-level cities in the Yangtze River Economic Belt from 2011 to 2020, this study first measured the agricultural carbon emissions, agricultural non-point source pollution, and ecological value of grain cultivation, then constructed a calculation model that included both desired and non-desired outputs to measure the ecological total factor productivity of grain and finally applied the super-efficient Slacks-Based Measure (SBM) model and the Global Malmquist-Luenberger total factor production index to calculate and analyze the ecological total factor productivity of grains in the Yangtze River Economic Belt. The results showed that: 1) the ecological total factor productivity of grain in the Yangtze River Economic Belt showed an overall growth trend from 2012 to 2020, with an average annual growth rate of 0.98%. The decomposition index of the ecological total factor productivity of grain showed that the technical efficiency was 0.9998, less than 1, whereas the technical progress index was 1.0273, greater than 1. The decomposition index indicated that the growth of the ecological total factor productivity of grain in the Yangtze River Economic Belt relied mainly on technical progress rather than technical efficiency. 2) From the perspective of spatiotemporal characterization, the ecological total factor productivity of grain in all prefecture-level cities in the Yangtze River Economic Belt achieved a more obvious improvement from 2012 to 2020, indicating that the green and sustainable development of grain in this region had achieved relatively good results. In terms of the decomposition indicators of the ecological total factor productivity of grain, the technical efficiency of all prefecture-level cities did not show a clear pattern, whereas the technical progress indexes of each prefecture-level city showed a continuous improvement trend. 3) In terms of regional comparison, the ecological total factor productivity of grains in the upstream area of the Yangtze River was the highest during the study period, reaching 1.0189, followed by the midstream region (1.0111); the lowest was in the downstream region (1.0014). Nevertheless, the ecological total factor productivity of grains increased in all three regions over time. Therefore, in the process of promoting sustainable grain production in the Yangtze River Economic Belt, it is essential to attach great importance to the role of technical progress and compensate for the shortcomings of technical efficiency as soon as possible.