It is an effective measure to estimate groundwater storage anomalies (GWSA) by combining Gravity Recovery and Climate Experiment (GRACE) data and hydrological models. However, GWSA results based on a single hydrological model and GRACE data may have greater uncertainties, and it is difficult to verify in some regions where in situ groundwater-level measurements are limited. First, to solve this problem, a groundwater weighted fusion model (GWFM) is presented, based on the extended triple collocation (ETC) method. Second, the Shiyang River Basin (SYRB) is taken as an example, and in situ groundwater-level measurements are used to evaluate the performance of the GWFM. The comparison indicates that the correlation coefficient (CC) and Nash-Sutcliffe efficiency coefficient (NSE) are increased by 9–40% and 23–657%, respectively, relative to the original results. Moreover, the root mean squared error (RMSE) is reduced by 9–28%, which verifies the superiority of the GWFM. Third, the spatiotemporal distribution and influencing factors of GWSA in the Hexi Corridor (HC) are comprehensively analyzed during the period between 2003 and 2016. The results show that GWSA decline, with a trend of −2.37 ± 0.38 mm/yr from 2003 to 2010, and the downward trend after 2011 (−0.46 ± 1.35 mm/yr) slow down significantly compared to 2003–2010. The spatial distribution obtained by the GWFM is more reliable compared to the arithmetic average results, and GWFM-based GWSA fully retain the advantages of different models, especially in the southeastern part of the SYRB. Additionally, a simple index is used to evaluate the contributions of climatic factors and human factors to groundwater storage (GWS) in the HC and its different subregions. The index indicates that climate factors occupy a dominant position in the SLRB and SYRB, while human factors have a significant impact on GWS in the Heihe River Basin (HRB). This study can provide suggestions for the management and assessments of groundwater resources in some arid regions.