The Nanyangtian W deposit, located in the Laojunshan ore concentration district, is the largest W deposit in the southeastern Yunnan, China. The latest chronological studies revealed that there are two-periods (Late Triassic and Early Cretaceous) skarnization in this deposit. Skarns are represented by the layered garnet–diopside skarn and quartz–garnet–vesuvianite–scheelite veined one, respectively. In this study, based on the field and microscopic mineralogical observations, we have identified three types of garnets including the layered type (Stage 1), massive and quartz vein type (period 2) garnets. The in situ analytical results of major and trace elements of garnets and vesuvianites of different stages indicate that all garnets of two periods belong to the grossularite-almandine solid solution series with slight compositional variation from Gro₉₅Alm₅ to Gro₈₅Alm₁₄, and the vesuvianite is characterized with enriched Al. The BSE images show that there is no growth zonation in both garnet and vesuvianite minerals indicating that they were formed in a relatively closed and stable hydrothermal fluid environment. The existence of REE in garnet is mainly controlled by two substitution mechanisms of [REE³⁺]^VII+[Y²⁺]^VI→[X²⁺]^VII+[Y³⁺]^VI and [REE³⁺]^VII+[Z³⁺]^IV→[X²⁺]^VII+[Si⁴⁺]^IV. The certain positive correlation between Na and REE in vesuvianite indicate that the REE substitution mechanism could be 2Ca²⁺ ↔ REE³⁺+Na⁺. The layered garnets are obviously depleted in HREE, with positive Eu anomalies, and relatively high contents of U and HFSE, indicating that the early-period skarn was formed under a relatively reduced, acidic and low Water–Rock ratio fluid condition. The quartz-vein type garnets are obviously depleted in LREE but enriched in HREE, with negative Eu anomalies, and relatively low contents of U and HFSE, and vesuvianite of the same stage has dramatic negative Ce anomalies, indicating that the late-period skarn was formed under a relatively oxidized, neutral to weak alkaline and high Water–Rock ratio fluid condition. The reduced and acidic fluid environment during the Late Triassic period is not conducive to the precipitation of scheelite, leading to that W occurred mainly in skarn minerals in form of the isomorphic substitution. During the Early Cretaceous period, the weakly alkaline, strongly oxidized, and high Water-Rock ratio characterized late-stage W-rich magmatic hydrothermal fluid is conducive to the precipitation of scheelite which is finally resulted in the the large-scale W mineralization.