The crust-lithosphere structure, especially the discontinuities such as Moho and lithosphere-asthenosphere boundary (LAB), is important in the investigation of geodynamic process implications and tectonic evolution of the lithosphere and regional seismic activity. We stacked the S receiver functions from 51 permanent broad-band stations to investigate the crust-lithosphere structures beneath the southeastern edge of the Tibetan Plateau and further discussed the mechanism of lower-crust earthquakes, the regional tectonics deformation characteristics, and the relationship between the two discontinuities and seismicity in this region. The results show that the Moho depth increases from 40 to 52 km beneath the Sichuan Basin to 56–74 km on the both western side of the Longmenshan (LMS) fault and Anninhe-Zemuhe fault. The LAB depth ranges from 130 to 170 km beneath the Sichuan Basin, and a shallow belt ranges from 100 km to 130 km around the Sichuan Basin. On the Moho depth contour map, 374 moderate earthquakes that accounted for 72.2%, corresponding to the depth range of 44–52 km and 60–68 km on the both sides of a narrow strip (longitude 102°~104°). On the LAB depth contour map, 321 earthquakes accounted for 62.15% in the depth range of 130–150 km. The variation of LAB corresponds to the increasing crustal thickness, intensive lower crustal earthquakes (hypocenters about 60 km and magnitude 4.0 ≤ Ms. ≤ 4.9) and surface abrupt elevations. It implied that Normal strong earthquakes generate the lower crustal earthquakes or aftershocks that resulted in the shear zones where fluid-induced metamorphic transformations, the eclogitization of dry granulite, and further affect the crustal thickness and deformation to control the spatial distribution of deep faults and seismicity.