Apatite grains from the No. 2 porphyry Cu–Au deposit in the Xiongcun district of Tibet, China, have a range of physical and compositional features. This study investigates the potential use of apatite associated with hydrothermal alteration as a tool for mineral exploration. In situ textural, cathodoluminescence (CL), and chemical analyses were performed on thin sections containing apatite from various alteration zones in the deposit. No clear variation was seen in apatite from rocks of the potassic, sodic–calcic, chlorite–sericite, phyllic, and propylitic alteration zones using visible light and scanning electron microscopy; however, distinct variations were observed in optical cathodoluminescence (OP-CL) (dark yellow to green, orange to green, yellow–brown to green, yellow-orange to brown, and light yellow–brown to green luminescence for the respective zones). The alteration-related differences in luminescence were a result of the interaction between Fe and Mn; the Na and Cl contents; and depletion in total heavy rare earth elements (ΣHREE) and Y. The variations in the REE contents of apatite from different types of altered rock record reactions with Cl- and F-rich fluids. The partitioning behavior of Cl between apatite and hydrothermal fluids is influenced by pressure, temperature, pH, and fluid composition, whereas the partitioning of F between apatite and fluids is dependent on the fluid composition and not the temperature. At high temperatures, Eu3+ is reduced to Eu2+, which results in negative Eu anomalies in apatite from the potassic-altered rocks and propylitic-altered rocks. Apatite grains in the sodic–calcic-altered rocks and chlorite–sericite-altered rocks show a similar enrichment in light REEs (LREEs) that resulted from REE and Y incorporation as follows: Na+ + (Y + REE)3+ = 2Ca2+. Apatite grains in the phyllic-altered rocks are enriched in the middle REEs. This study confirms that the luminescence, chemical composition (including Fe, Mn, Na, Cl, ΣHREE, and Y contents), and REE patterns of apatite can be affected by hydrothermal alteration; therefore, these results may be used to constrain the evolution of ore-forming hydrothermal fluids and may offer an effective tool for mineral exploration.