Water resources are rich on the Tibetan Plateau, with large amounts of glaciers, lakes, and permafrost. Terrestrial water storage (TWS) on the Tibetan Plateau has experienced a significant change in recent decades. However, there is a lack of research about the spatial difference between TWSC and lake water storage change (LWSC), which is helpful to understand the response of water storage to climate change. In this study, we estimate the change in TWS, lake water storage (LWS), soil moisture, and permafrost, respectively, according to satellite and model data during 2005−2013 in the inner Tibetan Plateau and glacial meltwater from previous literature. The results indicate a sizeable spatial difference between TWSC and LWSC. LWSC was mainly concentrated in the northeastern part (18.71 ± 1.35 Gt, 37.7% of the total) and southeastern part (22.68 ± 1.63 Gt, 45.6% of the total), but the increased TWS was mainly in the northeastern region (region B, 18.96 ± 1.26 Gt, 57%). Based on mass balance, LWSC was the primary cause of TWSC for the entire inner Tibetan Plateau. However, the TWS of the southeastern part increased by 3.97 ± 2.5 Gt, but LWS had increased by 22.68 ± 1.63 Gt, and groundwater had lost 16.91 ± 7.26 Gt. The increased TWS in the northeastern region was equivalent to the increased LWS, and groundwater had increased by 4.47 ± 4.87 Gt. Still, LWS only increased by 2.89 ± 0.21 Gt in the central part, and the increase in groundwater was the primary cause of TWSC. These results suggest that the primary cause of increased TWS shows a sizeable spatial difference. According to the water balance, an increase in precipitation was the primary cause of lake expansion for the entire inner Tibetan Plateau, which contributed 73% (36.28 Gt) to lake expansion (49.69 ± 3.58 Gt), and both glacial meltwater and permafrost degradation was 13.5%.