The Chang’E-6 (CE-6) mission successfully returned 1935.3 g of lunar soil samples from the Apollo basin within the South Pole–Aitken basin. One of its scientific objectives is to investigate the subsurface structure and regolith thickness at the landing site. Using remote sensing datasets, we estimated the regolith and basalt thicknesses at the landing site by employing the crater morphology method and crater excavation technique. A total of 53 concentric craters and 108 fresh craters with varying excavation depths were identified. Our results indicate that the regolith thickness at the CE-6 landing site ranges from 1.1 to 7.0 m, with an average thickness of 3.5 m. Beneath the regolith, the basalt layer consists of high-Ti basalt overlaying low-Ti basalt, with a total thickness of approximately 64 to 82 m, of which the high-Ti basalt layer accounts for about 22 to 30 m. Based on the local geological history, we proposed a stratigraphy at the CE-6 landing site. These findings provide valuable geological context for interpreting the Lunar Penetrating Radar data and analyzing the returned samples.