The Nanyangtian W deposit, located in the Laojunshan district, is the largest W deposit in southeastern Yunnan, China. However, before that, the mineralization age of this deposit is still controversial, since the absence of suitable dating minerals and methods. In this study, garnet and vesuvianite, the typical skarn minerals, and scheelite, the dominant ore mineral at Nanyangtian, were selected for LA–ICP–MS U–Pb dating to directly constrain the ages of skarn and W mineralization. As a result, two layered garnet samples together yield a Tera–Wasserburg lower intercept age of 203.2 ± 8.7 Ma, whereas two vein-type vesuvianite samples yield ages of 144.4 ± 3.7 Ma and 145.9 ± 3.1 Ma, identical within error to the ages of 141.5 ± 7.2–145.5 ± 2.9 Ma obtained from micro-disseminated and veinlet-like scheelite. The above dating results and the geological observations that ore-barren layered garnet cut by later quartz–scheelite–(garnet)–(vesuvianite) hydrothermal veins suggest two stages of skarnization in the Nanyangtian deposit (ca. 203 Ma and ca. 141–146 Ma, respectively), whereas the W mineralization occurred during ca. 141–146 Ma. It is inferred that the age of ∼203 Ma is related to Indosinian regional metamorphism and associated migmatization-hydrothermal activity. Nevertheless, the ages of 141–146 Ma, obviously older than those of the adjacent Laojunshan granitic pluton (∼83–97 Ma) and its associated Dulong Sn–Zn polymetallic deposit (∼82–96 Ma), are possibly attributable to another unrevealed magmatic-hydrothermal system at depth, as a result of Paleo-Pacific subduction during the Early Cretaceous period. A two-period superimposed mineralization model is thus proposed at Nanyangtian. Based on all reported age data, four major magmatic-metallogenic episodes ranging from ca. 445–410 Ma, 215–203 Ma, 152–140 Ma to 100–75 Ma have been determined in the Laojunshan district.