Abstract This paper presents a systematic study of late Cretaceous to early Tertiary magmatism in the eastern Gangdese batholith (Lhasa–Nyingchi segment), the southern Lhasa terrane, southern Tibet. Based on zircon U–Pb age, rock association and geochemistry, the magmatism can be divided into three stages: 95–86 Ma (stage-1), 85–73 Ma (stage-2) and 68–60 Ma (stage-3), with a short magmatic quiescence or gap of ~ 73–69 Ma. The stage-1 is composed mainly of intermediate-mafic rocks, including norite, gabbro, diorite, charnockite and subordinate granodiorite, whereas the stage-2 consists largely of felsic rocks including tonalite, granodiorite, monzogranite and granite. In contrast, the stage-3 comprises a wide range of rock types from gabbro to granite. All these samples show I-type geochemical characteristics, with high zircon Hf isotope ratios [eHf(t) = + 7.1–13.0], medium-K calc-alkaline and metaluminous to weakly peraluminous features. Stage-1 granitic rocks show low Sr/Y (31–43) and (La/Yb)N (6.3–8.3) ratios, in contrast to stage-2 that show gradually increasing Sr/Y (47–450) and (La/Yb)N (6–38) ratios. Their magma temperatures, constrained by titanium-in-zircon thermometer, decrease from 740–719 °C (stage-1) to 685–628 °C (stage-2). These are consistent with an interpretation of progressive magma source deepening coupled with crustal thickening. Stage-3 granitoids, in turn, show reduced Sr/Y (3–40) and (La/Yb)N (3.5–17.6) ratios and elevated magma temperatures (755–676 °C), suggesting a high temperature–low pressure melting condition and thus a shallow magma source which may imply the presence of thinner crust. The contrasting temperature–pressure conditions between stage-2 and stage-3 magmatism suggest an event of crustal thinning, which we interpret through a synthesis of other lines of geologic evidence to have resulted from a lithospheric delamination of the Lhasa terrane in the latest Cretaceous. In conclusion, the Lhasa terrane underwent continuous crustal thickening in the late Cretaceous and lithospheric delamination in the latest Cretaceous. This implies that the overthickened crust of southern Tibet is generated in the Cenozoic.