An atmospheric effect is a main error source that affects interferometric measurements. When a ground-based multiple-input multiple-output (GB-MIMO) radar, i.e., a specific type of GBsynthetic aperture radar (GB-SAR), was utilized to continuously monitor an open-pit mine, the interferometric phases of some interferograms were complexly space-variant due to time-variant weather conditions. The conventional method of atmospheric phase (AP) compensation was no longer applicable. This paper proposes an improved compensation method of a time-space variant AP applied to time-series GB-SAR images. The permanent scatterers (PSs) were classified into three types based on their different spatial properties: The noise-dominant PS (NPS), the deformationdominant PS (DPS), and the atmospheric effect-dominant PS (APS). The NPSs were firstly rejected based on the differential phase analysis of neighboring PSs. The DPSs were then rejected based on the cluster partition and selection. With the APSs, the space-variant AP was estimated with a spatial interpolation. To validate the feasibility of the proposed method, short-term and long-term experimental datasets were processed. Comparisons with a conventional method proved that the proposed method can well reduce AP errors and avoid the misunderstanding of motional areas.