Understanding vegetation water availability can be important for managing vegetation and combating climate change. Changes in vegetation water availability throughout China remains poorly understood, especially at a high spatial resolution. Standardized Precipitation Evapotranspiration Index (SPEI) is an ideal water availability index for assessing the spatiotemporal characteristics of drought and investigating the vegetation-water availability relationship. However, no high-resolution and long-term SPEI datasets over China are available. To fill this gap, we developed a new model based on machine learning to obtain high-resolution (1 km) SPEI data by combining climate variables with topographical and geographical features. Here, we analyzed the long-term drought over the past century (1901–2020) and vegetation-water availability relationship in the past two decades (2000–2020). The century-long drought trend analyses indicated an overall drying trend across China with increasing drought frequency, duration, and severity during the past century. We found that drought events in 1901–1961 showed a larger increase than that in 1961–2020, with the Tibetan Plateau showing a significant drying trend during 1901–1960 but a wetting trend during 1961–2020. There were 13.90% and 28.21% of vegetation in China showing water deficit and water surplus respectively during 2000–2020. The water deficit area significantly shrank from 2000 to 2020 across China, which is dominated by the significant decrease in water deficit areas in South China. Among temperature, precipitation, and vegetation abundance (LAI), temperature is the most important factor for the vegetation-water availability dynamics in China over the past two decades, with high temperature contributing to water deficit. Our findings are important for water and vegetation management under a warming climate.