The Central Asian Orogenic Belt underwent complex tectonic processes and is one of the most intensely accretionary areas globally. Porphyry copper deposits within the belt were likely subjected to deformation during tectonic processes. The Bainaimiao Cu-Au deposit is a typical example of a deformed porphyry deposit whose formation processes include a porphyry emplacement (Event I), a greenschist facies metamorphism (Event II), and a brittle deformation (Event III). Geochronology and trace element geochemistry of zircon, volatiles of magmatic apatite, along with the assemblages, textures, abundances, and compositions of phyllosilicates from these three events were investigated to unveil the physicochemical conditions under which the key geological events relevant to the deposit formation took place. LA-ICP-MS zircon U-Pb dating shows that the granodiorite porphyry in the northern and southern zones formed at 447.4 ± 1.6 to 445.8 ± 3.6 Ma and 436.1 ± 3.8 to 434.1 ± 3.3 Ma, respectively. The granodiorite porphyry in the northern zone has higher oxygen fugacity and Clmelt content but similar Smelt and Fmelt contents compared to the granodiorite porphyry in the southern zone. Microscopic and mineralogic observations point to Event I to be of high plagioclase (22–67 vol%) and quartz (6–40 vol%) content with a range of hydrothermal minerals related to potassic, phyllic, and propylitic alterations. Event II features high amphibole (38–83 vol%) or epidote-chlorite (up to 77 vol%) content with minerals precipitating along the schistosity planes. Event III is characterized by wide veins (3–80 cm) and the highest quartz (61–65 vol%) and calcite (12–19 vol%) content. Geothermometry results show the temperature of potassic and phyllic alterations of Event I to be ∼622 °C and ∼288 °C, respectively. Based on geothermometry and P-T pseudosections, the temperatures of metamorphism and metallic precipitation of Event II were ∼271–634 °C and 297–328 °C, respectively. Both mechanical and chemical mobilization of metallic elements results in Cu mineralization during Event II. The metallic precipitation temperatures of Event III spanned from 297 to 328 °C according to chlorite geothermometry. The ratios of Fe3+/Fetotal and Mg/(Mg + Fetotal) of biotite, chlorite Fe/(Fe + Mg), and white K-mica composition show the mineralizing fluid of Event III to be the most oxidized while that of Event II is the most reduced, F-rich and features the lowest water/rock ratio. This study suggests that deformation processes can increase the Cu mineralization grade of the deformed porphyry deposits through mobilization and re-precipitation of metallic elements.