The Naruo Cu (Au) deposit is currently the third biggest in the Duolong ore concentrated area in northwestern Xizang (Tibet). The study on chronology of petrogenesis an mineralization, metallogenic geological background, and so on, have been conducted comprehensively, but research on spatial alteration zoning and magmatic development process is quite limited. The apatite of the Naruo deposit serve as the study subject in this work. The study of apatite mineralogy and major elements geochemistry is carried out on the basis of a large number of drilling scientific research catalogs, and the colorful cathodoluminescence features of the apatite in the Naruo deposit are described. The coupling connection with alteration zone indicates the development stage of ore- bearing magma as well as the redox state change rule. The apatite in the Naruo deposit is mostly yellow—brown, green—bright yellow, and gray- black, correlating to unmodified magma, potassic alteration, and sericitization alteration, respectively. Those relationship validated the spatial alteration zoning structure of the “double potassic zone” of the Naruo deposit porphyry system, which was redefined in this work. The main element test results of apatite via EPMA show that CaO = 53.5%~56.5%, P2O5 = 39.5%~42%, F = 1.26%~3.24%, Cl = 0.01%~1.99%, SO3 = 0~1.28%, and the calculated XF= 0.68~1.76, XCl = 0.001~0.58, XOH = 0.21~1.05. The change trend of elements such as volatile components (F, Cl, OH) and SO3 of apatite in different types and stages reflects the process of gas saturation fluid exsolution metal precipitation in the magmatic hydrothermal evolution of the Naruo deposit, and reveals the nature of high oxygen fugacity of the ore- forming magma. In addition, the zonal magmatic apatite reflects that the cryptoexplosive breccia system has developed three stages of magmatism, and indicates that the I and III stages of magmatism are characterized by high oxygen fugacity, which are more closely related to mineralization. This paper therefore holds that the multiphase magmatic hydrothermal alteration superimposed porphyry copper deposits can also benefit greatly from apatite inversion of the magmatic hydrothermal evolution process and auxiliary determination of alteration zoning in addition to the concealed porphyry copper deposits in the till covered area.