The Xiongcun district, a unique area where oxidized porphyry copper-gold deposits (OPCD) and reduced porphyry copper-gold deposits (RPCD) coexist, is located in the central part of the Gangdese porphyry copper belt (GPCB) in Tibet, China, and hosts the only known mineralization related to the Neo-Tethyan oceanic subduction. Apatite and zircon major and trace elements, in situ oxygen isotopes in zircon from fertile quartz diorite porphyry (QDP) of the No. I deposit, fertile hornblende quartz diorite porphyry (HQDP) of the No. II deposit, and barren hornblende quartz diorite porphyry with coarse quartz eyes (QQDP) in the Xiongcun district were determined by EPMA, LA-ICP-MS, and SHRIMP II ion microprobe to investigate the petrogenesis, magma oxidation state, and mineralization differences between the No. I and No. II deposits, as well as the potential of apatite as a metallogenic indicator. The results from this study show that a combination of REE, Ti, oxygen isotopes, and the Th/U ratios in zircon and REE as well as Sr in apatite can be used to track the magma compositions and crystallization histories in porphyry systems. Multiple indicators, including the apatite SO3 content, apatite Mn oxybarometer, and zircon Ce4+/Ce3+ ratio, indicate that (1) the parental magmas of fertile QDP and HQDP containing Cu and Au mineralization were more reduced than that of barren QQDP; (2) despite barren QQDP having higher oxygen fugacity than QDP and HQDP, the lower Cu and water contents in the magma result in a lower potential for ore formation; and (3) the similar oxidation states of QDP and HQDP show that the mineralization differences between RPCD (No. I deposit) and OPCD (No. II deposit) were not caused by the oxidation states of the magmas but were likely caused by the different processes of hydrothermal fluid evolution. Apatite grains from fertile porphyries (QDP and HQDP) have much higher Cl/F ratios than those from barren porphyry (QQDP), indicating that the Cl/F ratio of apatite can be used as a proxy for porphyry Cu-Au mineralization related to the Jurassic porphyry intrusions in the Gangdese porphyry copper belt.