Water resource and carbon emission involved in grain production in mainland China are redistributed among provinces as the grain was transported in recent years. This study first calculated the water consumption and carbon emission during the growth of grain crops based on the water-carbon footprint theory, and then used the social-equity method to calculate the inter-regional grain virtual water and virtual carbon flow. Finally, the regional and national trends in water saving and carbon emission reduction were calculated based on the spatial and temporal differences in grain planting among provinces. In terms of virtual water-carbon, from 2000 to 2017, the amount of the inter-provincial grain virtual water flow increased from 717.4 × 108 m3 to 1472.6 × 108 m3. Heilongjiang and Guangdong are the provinces with the largest amount of grain virtual water outflow (670.9 × 108 m3) and inflow (402.8 × 108 m3) in 2017, respectively. And the total inter-provincial grain virtual carbon flow increased from 2362.7 × 104 t CO2e to 12,680.6 × 104 t CO2e. Grain transport leads to water saving and carbon emission reduction, the amount of water saving increased from 25.6 × 108 m3 to 77.0 × 108 m3 and the carbon emission reduction increased from 2.4 × 104 t CO2e to 847.4 × 104 t CO2e from 2000 to 2017. Based on research results and from the perspective of socio-hydrology combined with water saving and carbon emission reduction, the regions could optimize the integration of water saving, carbon emission reduction, and sustainable development based on coordinating the grain planting structure according to their own climatic condition, soil and water resource condition, and socioeconomic condition.