Abstract: To explore the sustainable status of agricultural water withdrawal in China, the spatial and temporal changes of agricultural water use in 31 provincial administrative regions from 1998 to 2020 were calculated and analyzed, at the perspective of freshwater resources as a key natural capital, which combining 3D water footprint, downscaled planetary boundaries and decoupling analysis. The results showed that the overall agricultural water withdrawal in China was good, but the sustainable status of regional agricultural water withdrawal varied greatly. The contradiction between water supply and demand was more prominent in North China, East China and Northwest China, where precipitation was low or social and economic water withdrawal was high, while the sustainable situation of water resources in Southwest China and South China, where precipitation is abundant, was better. Under the influence of residents’ increasing awareness of water conservation and policy constraints, agricultural water sustainability in Beijing, Hebei, Shanxi, and Shanghai was becoming better; under the influence of large inter-annual differences in precipitation and changes in the proportion of agricultural water use, agricultural water sustainability in Liaoning, Jiangsu, Shandong, Henan, and Gansu was abruptly changing, and there was no obvious pattern of change in the occupancy relationship between stocks and flows. Zhejiang showed the best performance of agricultural water-economy relationship, while Beijing showed the opposite; the worst type of agricultural water-economy 6 emerged in Beijing and Shanghai frequently after 2014. The contradiction between economic development and resources environment was becoming more and more severe. The research results can provide reference for agricultural water use and plantation planning.