The ca. 90 Ma (92−84 Ma) high-Sr/Y intrusions in the western central Lhasa terrane (WCLT) of the Tibetan Plateau record critical information about the late Mesozoic crustal architecture of the Lhasa terrane and may have provided favorable conditions for porphyry mineralization. However, conflicting geodynamic processes have been proposed, and their mineralization potential is unclear. Here, we report the newly discovered Banongzuosi porphyry-skarn Mo-Cu deposit and Qielong skarn Cu-Au and Rongqing porphyry-quartz vein-type Mo mineral prospects. They provide important constraints on the generation of the ca. 90 Ma high-Sr/Y magmas and their associated mineralization potential. Then, integrated studies of the ca. 90 Ma intrusions are performed to address the above issues. Dating shows that intrusions and mineralization in the three areas occurred at 92.4−84.1 Ma. Based on whole-rock geochemistry, the high-Sr/Y intrusions can be divided into low- and high-Mg#-Cr ones. Zircon Hf isotopic data indicate that both ancient and juvenile lower crust existed in the WCLT, with significant juvenile components in the high-Mg# and Cr-rich intrusions. The crustal thickness calculated from the zircon trace element data suggests that the WCLT had thickened crust (>64 km) with local areas thinned by lower crustal delamination at ca. 90 Ma. Regional thickening and local lower crustal delamination formed the low- and high-Mg#-Cr intrusions, respectively. Whole-rock and zircon trace element data reveal that most of the ca. 90 Ma high-Sr/Y intrusions are hydrous and oxidized. The thickened crust resulted in high H2O contents and fO2 of intrusions and promoted porphyry-skarn mineralization. However, crustal thinning and contamination by reduced Precambrian basement decreased the magma fO2 and hindered mineralization. The advantageous tectonic setting and high H2O and fO2 led to the ca. 90 Ma high-Sr/Y intrusions having the potential to form collisional porphyry-skarn Cu-Au-Mo deposits.