Accurately understanding flood evolution and its attribution is crucial for watershed water resource management as well as disaster prevention and mitigation. The source region of the Yellow River (SRYR) has experienced several severe floods over the past few decades, but the driving factor influencing flood volume variation in the SRYR remains unclear. In this study, the Budyko framework was used to quantify the effects of climate change, vegetation growth, and permafrost degradation on flood volume variation in six basins of the SRYR. The results showed that the flood volume decreased before 2000 and increased after 2000, but the average value after 2000 remained lower than that before 2000. Flood volume is most sensitive to changes in precipitation, followed by changes in landscape in all basins. The decrease in flood volume was primarily influenced by changes in active layer thickness in permafrost-dominated basins, while it was mainly controlled by other landscape changes in non-permafrost-dominated basins. Meanwhile, the contributions of changes in potential evapotranspiration and water storage changes to the reduced flood volume were negative in all basins. Furthermore, the impact of vegetation growth on flood volume variation cannot be neglected due to its regulating role in the hydrological cycle. These findings can provide new insights into the evolution mechanism of floods in cryospheric basins and contribute to the development of strategies for flood control, disaster mitigation, and water resource management under a changing climate.