Southernmost Tibet exhibits an anomalously twice the normal thickness of average continental crust. There is no available theory to explain and the driving mechanism remains uncertain. Here, we interpret a north-striking, 180 km-long deep seismic reflection profile traversing the southern Lhasa terrane (SLT) to the central Lhasa terrane (CLT). In addition to reflections showing subducting Indian crust, our results reveal lateral heterogeneity between the SLT and CLT, where north-dipping reflections beneath the CLT outline a tilted crystalline basement, while the non-reflective domain beneath the SLT represents homogeneous juvenile crust. Our integrated analysis leads to models calling upon episodic magmatism onto the southern margin of the basement to result in progressive construction of the SLT. We hypothesize that this crustal thickening via crustal-scale magma accretion contributed to surface uplift of the southern margin of the Tibetan plateau and leading to the development of the vast internal drainage system of Tibet.