Based on the grey water footprint, the ecological compensation amount of the Yangtze River Basin from 2009 to 2020 was quantified, to provide support for improving the ecological compensation and protection mechanism of the Yangtze River Basin. The grey water footprint and load coefficient of 15 provinces, 2 municipalities, and 2 autonomous regions in the Yangtze River Basin from 2009 to 2020 were calculated from three aspects: agriculture, industry, and life. The ecological compensation standards of each province (municipality directly under the central government and autonomous region) in the basin were calculated using the zero-sum model and the ecological compensation standard correction index. The results show that: 1) From 2009 to 2020, the overall gray water footprint in the Yangtze River Basin increased first and then decreased, and reached a peak of 913.144 billion m3 in 2015. The gray water footprint decreases more significantly over time in the middle and lower reaches of the basin. Most of the provinces (municipalities and autonomous regions) in the types of regions with larger gray water footprint loading coefficients in the basin and at the same time less water resources distribution has shown a decreasing trend in gray water footprint loading coefficients in 2019-2020, which implies a weakening of the pressure on freshwater resources. The total absolute value of river basin ecological compensation standards has shown a fluctuating trend within a relatively stable range, with the lowest value of 57.092 billion yuan in 2011 and the highest value of 109.045 billion yuan in 2019. 2) The average annual graywater footprint for agriculture within the Yangtze River Basin is largest in the upper reaches, followed by the middle reaches and the lower reaches in that order. The average annual graywater footprint of industry and domestic within the Yangtze River Basin is largest in the middle reaches, followed by the lower reaches and the upper reaches in that order. Agriculture has the largest share of the regional graywater footprint, followed by domestic and industrial graywater footprints in that order. The largest range of average ecological compensation thresholds within the Yangtze River Basin is in the middle reaches, followed by the lower reaches and upper reaches in that order. The largest cumulative deficit eco-compensation standards are in the downstream region, followed by the upstream region and the midstream region in that order. The largest cumulative surplus eco-compensation standards are found in the midstream region, followed by the upstream region and the downstream region in that order. Basin ecological compensation standards in general show a cumulative deficit greater than a cumulative surplus. 3) The absolute error between the theoretical total value and the actual total investment value of the ecological compensation standard in the Yangtze River basin is 186 million yuan, and the relative error is only 0.22%. The research results reflect the quantitative relationship of ecological compensation among provinces (municipalities directly under the central government and autonomous regions) in the Yangtze River Basin, and demonstrate the high feasibility of the research methodology.