The carbon sequestration of food crops is of great significance to slow down agricultural greenhouse gas emissions in agricultural production and management. This paper analyzes the dynamic change and regional differences of net carbon sequestration of food crops from temporal and spatial perspectives for the case study area of the Yangtze River economic belt (YREB) in China. We use the calculation formula of carbon sequestration and carbon emission to calculate the net carbon sequestration in the Yangtze River economic belt. On this basis, we analyze the dynamic trend and regional differences of net carbon sequestration in the Yangtze River economic belt. Furthermore, we use the Gini coefficient to measure the quantitative gap of net carbon sequestration of grain crops in different regions of the Yangtze River economic belt. The results show that: (1) from 2000–2018, the net carbon sequestration of food crops keeps rising within the studied area, while the carbon emission shows a fluctuating downward trend; (2) remarkable regional differences in the net carbon sequestration of food crops have occurred, and most provinces (cities) show an upward trend for the studied area; (3) the unequitable distribution of net carbon sequestration of food crops is clearly displayed in the upper, middle, and lower reaches of the studied area. Moreover, the most uneven place is located on the lower reaches, and the least uneven place is in the upper reaches. These findings are important points of reference for reducing the carbon emissions of the agricultural industry in the Yangtze River economic belt of China and in China more generally.