Large-scale vegetation restoration has markedly enhanced ecosystem services in the Three-North (TN) region, concurrently exacerbating the pre-existing water resource crisis stemming from climate change in this arid domain. However, the specific contributions of climate and vegetation changes to the evolution of water resources in the TN region have yet to be elucidated. This study leverages data from the Gravity Recovery and Climate Experiment (GRACE) and its Follow-on mission (GRACE-FO), specifically the terrestrial water storage anomaly (TWSA) from 2003 to 2021. We identify two TWSA rising (TWSA_rⅠ and TWSA_rⅡ) and two declining (TWSA_dⅠ and TWSA_dⅡ) hotspots in the TN region. By exploring the relative importance of climate drivers and vegetation dynamics in influencing the temporal dynamics of TWSA, we found that vegetation restoration assumes a more pivotal role than climate factors in 45.2% of the total area within the identified hotspots, predominantly evident in TWSA declining hotspots. The heightened TWSA in TWSA_rⅠ and TWSA_rⅡ primarily stems from precipitation recharge, with precipitation-dominated areas constituting 19.3% of the area within the identified hotspots. Potential evapotranspiration dominates TWSA changes in only 4.6% of the region within the identified hotspots, primarily scattered in TWSA_dⅠ and TWSA_dⅡ. Furthermore, a comparative assessment of soil moisture and groundwater responses to environmental factors indicates that water storage at shallower layers is more responsive to climate factors, while the impacts of vegetation changes on TWSA are more discernibly reflected in water storage at deeper layers. These findings furnish scientific guidance for future ecological restoration planning and sustainable water resources management.