The Yellow River Basin and the Yangtze River Basin are the two most important watersheds in China, which consist of several key ecological function areas and are crucial in terms of economic contributions. The evaluation of the ecosystem service value and the quantitative acquisition of the regional ecological quality status are necessary for supporting the ecological protection and high-quality development of the two basins. By considering basic data and adopting different ecological function models, this study was carried out to evaluate the value of ecosystem services in the Yellow River Basin and the Yangtze River Basin from 2015 to 2018 in terms of provisioning services, regulating services, and cultural services. Additionally, analysis was conducted in combination with economic indicators. The results showed that there were great differences in the ecosystem patterns between the Yellow River Basin, where grassland accounted for 45% of land use, and the Yangtze River Basin, where forest accounted for 39% of land use. The values of the ecosystem services of the two basins had similar spatial distributions, with higher values upstream (west) followed by downstream (east) and lower values in the middle (central China). The total annual ecosystem value of the Yangtze River Basin was more than three times that of the Yellow River Basin. In addition, the ecosystem services value of most counties in both basins was higher than their GDP, and there was a positive trend of transforming ecological benefits into economic benefits in the Yangtze River Basin. This research provides a methodology for evaluating ecosystem valuation. The results are helpful for formulating and implementing eco-compensation and payments for ecosystem service policies among different regions in the basins, and the results lay a foundation for the spatial planning and high-quality development paths of key basin areas in China.