The South Pole–Aitken (SPA) basin is the oldest and largest impact structure on the Moon, and it gives particular insight on the lunar interior composition1–3. However, the surface of the SPA basin has been substantially modified by consequent impacts and basalt flooding. The exploration of the surficial material and the substructure of the SPA basin is one of the main scientific goals of the Chinese spacecraft Chang’E-4 that landed in the Von Karman crater inside the SPA basin4,5. Here we report the lunar penetrating radar profiles along the track of the lunar rover Yutu-2, which show a three-unit substructure at the landing site. The top unit consists of the ~12-m-thick lunar regolith and ~120 m multilayered ejecta that were delivered from several adjacent craters. The middle unit is the mare basalts filling the Von Karman crater. The lowest unit is another ejecta layer with a thickness of ≥200 m, likely from the Leibnitz crater. These discoveries fully support the local stratigraphy and geological explanation presented previously6. Our results reveal that the surface materials at the Chang’E-4 landing site are unambiguously dominated by the ejecta from the Finsen crater with a minor contribution from other neighbouring craters. The regolith measured by Yutu-2 is representative of the initial lunar deep interior materials, rather than the later erupted basalts. Three different layers can be distinguished in the first 500 metres of depth beneath the South Pole–Aitken basin on the Moon: a first layer made up by regolith and ejecta material from different craters, followed by a middle unit of mare basalts and finally a >200-m-thick layer of ejecta from the Leibnitz crater.