In DEM generation using interferometric synthetic aperture radar (InSAR), the ground control points (GCPs) for refinement and reflattening are usually selected by manual selection, field surveying, GPS points and existing basemaps, which may not be completely suitable for consequent processes. We proposed a new method (auto-PS-GCP) of GCP selection based on permanent scatterers, which automatically defines the thresholds for the coherence, amplitude, and amplitude dispersion index to select permanent scatterer as the GCPs. The GCP thinning (auto-PS-GCP-Thin) was further conducted considering the point density, distances among points and terrain conditions. We used a three-stage assessment that includes: (1) phase stability and intensity of the GCPs, (2) RMSEs of the elevations between GCPs and homonymous points in the reference DEM, and (3) generated DEM accuracy. Three areas respectively in the plain, hilly and mountainous regions were selected to verify the proposed methods. The assessment using both SRTM DEM andICESat-2 points shows that the DEM accuracy of auto-PS-GCP-Thin was improved by 20%∼30% for different areas compared to the manual, where the best DEM accuracy of 4.71 m was found in the plain area. It is concluded that the proposed methods are effective and reliable in various areas with different terrain conditions.