This paper aims to address the limitations of the distribution number and uniformity of Continuously Operating Reference Stations (CORS) and their impact on the reliability of inverting regional groundwater storage (GWS) based on Green’s function method and using global navigation satellite system (GNSS) data. A fusion method on the inversion of regional GWS changes from GNSS and the Gravity Recovery and Climate Experiment (GRACE) was proposed in this paper. Taking the Shaanxi–Gansu–Ningxia (SGN) region as an example, the in situ groundwater level data from ten CORS stations and eight wells were used for test analyses. In this paper, an atmospheric pressure model from the European Centre for Medium-Range Weather Forecasts (ECMWF), a global land data assimilation system (GLDAS), a WaterGAP global hydrology model (WGHM), and mean sea level anomaly (MSLA) data were used to quantitatively monitor the influence of vertical deformation caused by non-tidal environmental load. After deducing these loading deformations from the filtered time series of non-linear monthly geodetic height from the GNSS, the GWS changes in the SGN region from 2011 to 2014 were inverted. Meanwhile, the change in surface water storage from the GLDAS and WGHM models were removed from the terrestrial water storage (TWS) changes derived from GRACE. On this basis, the remove–restore theory in the Earth’s gravity field was introduced to both fuse the inversion results and obtain the regional GWS changes based on the fusion method. The results showed the following: (1) The local characteristics from the fusion results were more prominent than those of GRACE on the spatial scale, such as in the southwest and northeast in the study area. In addition, the fusion results were more uniform than those from GNSS, especially for the sparse and missing areas in which CORS stations were located, and the local effect was weakened. (2) On the time scale, compared with GRACE, the trends in GWS changes obtained from the fusion method and from GNSS inversion were roughly the same as the in situ groundwater level changes. (3) For the in situ groundwater wells “6105010031” and “6101260010”, the correlation coefficients of the fusion result were 0.53 and 0.56, respectively. The accuracy of the fusion method was slightly higher than that from GNSS, which indicates that the fusion method may be more effective for areas where CORS stations are missing or sparsely distributed. The methods in this paper can provide significant reference material for hydrodynamic research, sustainable management of water resources, and the dynamic maintenance of height data.