The Xiaorequanzi Cu deposit is located in the western part of the Dananhu–Tousuquan Island arc in eastern Tianshan, Xinjiang. It includes stratiform and epithermal-related veinlet mineralization. However, the genesis of this deposit remains controversial. Therefore, fluid inclusions, H–O isotopes, in situ S, and trace elements in pyrite were employed in this study to constrain the origins of the deposit. The Xiaorequanzi Cu deposit’s mineralization stages can be categorized into the following three phases: I. volcanogenic massive sulfide (VMS) mineralization; II. quartz–chalcopyrite–pyrite; and III. quartz–chalcopyrite–sphalerite stages. Fluid inclusion studies suggest that Stage I is distinguished by high-temperature (peak: 320–360 °C) and moderate-salinity (peak: 7–9 wt%) fluids belonging to the H2O–NaCl ± CO2 system. Stages II–III only exhibit vapor–liquid inclusions, with mineralizing fluids belonging to the medium-to-low-temperature (Stage II peak: 160–180 °C; Stage III peak: 120–130 °C) and medium-to-low-salinity (Stage II peak: 5–7 wt%; Atage III peak: 4–6 wt%) H2O–NaCl system. The H–O isotopic data suggest that mineralizing fluid in Stage I is a blend of magmatic and paleo-seawater sources, while in Stages II–III, meteoric water predominates, accompanied by low mineralizing temperatures. In situ S isotope results indicate that the source of mineralizing materials in Stage I (2.52–4.48‰) were magmatic rocks, whereas the markedly higher δ34S values in stages II–III (4.68–6.60‰) suggest sulfur isotope leaching from sedimentary rocks by meteoric water as the main source. The LA–ICP–MS data of pyrite in the Xiaorequanzi Cu deposit suggest that Py1 was formed through volcanic processes, whereas Py2 and Py3 exhibited epithermal characteristics. Throughout the mineralization process, a trend in increasing oxygen and decreasing sulfur fugacity occurred, accompanied by a decreased mineralization temperature. This observation corresponds with the temperature data derived from the fluid inclusions. Additionally, the principal components of different generations of pyrite segregated as two clusters representing the VMS (Stage I) and epithermal mineralization (stages II–III). In summary, based on comprehensive research and previous geochronological studies, it is suggested that the Xiaorequanzi Cu deposit experienced two mineralization stages. The early stage is related to the volcanic activity of the Early Carboniferous (354 Ma), whereas the later stage is associated with Carboniferous–Permian (266–264 Ma) volcanic intrusions.