Land subsidence has attracted widespread attention because of its potential hazards to sustainable urban development. The traditional methods for estimating land subsidence disregard the crucial aspect of altitude by analyzing spatial data solely on the 2D plane (longitude and latitude geographic coordinates). This research incorporates the altitude feature into the construction of the spatial matrix to develop a new method named spatially multiscale geographically weighted regression (SM-GWR) for a better estimation of land subsidence, enabling to determine the optimal bandwidth at 3D spatial scales. By adopting a 3D perspective, the new algorithm accurately fits settlement points based on spatial distances, addressing previous limitations of projecting points on a two-dimensional surface and ignoring height differences, thereby providing a more realistic depiction of spatial relationships. The satellite data is first used to monitor land subsidence through the small baseline subset synthetic aperture radar interferometry (SBAS-InSAR). Then, the SM-GWR model is developed to construct the 3D spatial weight matrix and update estimate parameters through back-fitting calibration. The proposed method's feasibility is confirmed through examples of land subsidence in China and Singapore. The case study results demonstrate that: (1) The SM-GWR model shows significant improvement in fitting land subsidence compared to the traditional method (R2 value of 0.908 and 0.934 in predicting annual subsidence and cumulative subsidence, respectively); (2) The contribution of the influencing factors is highly related to the nature properties and urban development of the city. The novelty of this study lies in the development of an SM-GWR model combined with satellite monitoring to achieve high-precision estimation of land subsidence, considering the 3D structure of spatial geographic data.