The northwestern China (NWC) generally suffers from severe water shortages. To improve the management and utilization of the limited water storage in NWC, it is crucial to explore the distribution and variation of water storage. Here, we obtained the variations of terrestrial water storage (TWS), surface water area (SWA), and groundwater storage (GWS) in NWC (which refers to Xinjiang Uyghur Autonomous Region in the study) from 2002 to 2018 based on multi-source satellite data, and analyzed the factors influencing water storage changes. The results indicated that (1) SWA exhibited an increasing trend with 40.90 km2/year from 2002 to 2018 based on main lakes/reservoirs and rivers water area in NWC, due to the increase of precipitation and glacier melting. TWS and GWS showed a decreasing trend with a mean rate of −1.25 mm/year and −1.08 mm/year from 2002 to 2018 in NWC, respectively, due to the increase of arable land area and water consumption. (2) SWA in northern and southern NWC showed a decrease (-0.72 km2/year) and an increase (51.14 km2/year) from 2002 to 2018, respectively. The different rates are due to regional precipitation and temperature variations. TWS in northern and southern NWC showed a declining of −0.14 mm/year and −1.94 mm/year, respectively. GWS in northern and southern NWC showed a declining of −0.55 mm/year and −1.72 mm/year, respectively. The differences are related to the greater evapotranspiration and irrigation water consumption in southern than northern NWC. This study enriches the information on water storage in NWC and provides useful guidance for local water resource management and protection.