Gengnai skarn deposit is located in southern middle Bangong Co-Nujiang River metallogenic belt, Tibet. It has good geological conditions for Fe and In mineralization. What’s more, it is the first time to find natural indium and jalindite in this deposit in China. The deposit formed in the dimetasomatism when the porphyritic monzonitic granite invaded the Langshan limestone, and the porphyritic monzonitic granite provided magmatic hydrothermal sources for the mineralization. The K2O/Na2O values of porphyritic monzonitic granite are in the range of 1.38~1.73, showing the characteristics of potassium-rich. The A/CNK values of porphyritic monzonitic granite are in the range of 1.02~1.05. Gengnai rock mass belongs to peraluminous granite, with S-type granite characteristics. Rittmann index (σ) values are in the range of 2.15~2.31, and the porphyritic monzonitic granite is a calc-alkaline rock series. In Gengnai porphyritic monzonitic granite,large ion lithophile elements such as Rb,Th are enriched,and elements such as Sr，Ba，P,Ti are poor. It has higher total REE(∑REE=108.03×10-6~258.74×10-6), and light and heavy REE has obviously fractionation with (La/Yb)N is 15.707 to 26.002. δEu=0.171~0.238,with medium negative Eu anomalies. Zircons in the porphyritic monzonitic granite are magmatic zircons. They are mostly columnar The Th/U values of zircons are in the range of 0.498~1.866, while the（La/Yb）N values are 0.00~0.29, light and heavy REE has obviously fractionation. The zircons have high positive Ce anomaly(δCe=4.32~1293.43) and medium negative Eu anomaly(δEu=0.06~0.13). The Gengnai rock mass occurred in the collision orogenic phase after the Bangong Co-Nujiang River ocean subducted to the South. Studies have shown that there is no correlation between indium and tin，also between indium and zinc，but it has positive correlation between indium and iron. Indium content values of the iron ore are in the range of 5.61×10-6~125.00×10-6, and the average is 49.01×10-6, indium exist in the form of independent mineral. The mineralization of iron, indium, bismuth are formed in the same period of hydrothermal activity, and they are all magmatic source. The zircon LA-ICP-MS dating results of the porphyritic monzonitic granite is 78.7±1.7 Ma, suggesting the porphyritic monzonitic granite was a product of late Yanshanian magmatism.