The Axi deposit is the largest low-sulfidation epithermal gold deposit in Chinese Western Tianshan, Central Asian Orogenic Belt. In this contribution, combined petrological observations, electron microprobe analysis (EMPA) and X-ray backscattered electron images (BSE) have been conducted on Fe-S-As minerals to reveal their textural and compositional evolution. Pyrite and arsenopyrite are ubiquitous. Their texture and composition show gradual changes with time. Four generations of pyrite can be identified, named Py1, Py2, Py3 and Py4 from early to late. The coarse-grained, euhedral to subhedral Py1 (mostly 100–300μm) from the quartz-chalcedony stage is the earliest, and predates gold mineralization. Sometimes they contain silicate and arsenopyrite (Apy1) inclusions. Compositionally, they are enriched in Pb (up to 0.60wt%), but depleted in As (0.06–7.61wt%, mostly <0.30wt%) and Au (0.01wt%–0.25wt%, mostly <0.10wt%). Subhedral to anhedral Py2 grains (50–1000μm) coexist with other sulfides such as chalcopyrite, sphalerite, galena and tetrahedrite in the quartz-polymetallic sulfides stage. They are unusually rich in Au (with a mean value of 0.06wt%), Ag (with a mean value of 0.04wt%), Cu (with a mean value of 0.21wt%) and As (with a mean value of 3.06wt%), implying a syn-mineralization feature. Subsequent Py3 occurs as very fine-grained disseminations of euhedral crystals (10–50μm) in quartz-polymetallic sulfides stage and carbonate-quartz stage. They display clear oscillatory zoning and contain arsenopyrite (Apy3), sphalerite and Sb-Te mineral inclusions. Their Au content vary greatly from 0.02wt% to 1.02wt%, with corresponding As content varying from 0.07wt% to 8.28wt%. The post-mineralization Py4 crystals (30–5000μm) mainly occur as foliated, sheaf, or radiaxial aggregates in carbonate-quartz stage. They have the lowest Au (with a mean value of 0.04wt%), As (with a mean value of 0.32wt%), Co (with a mean value of 0.04wt%) and Ni (with a mean value of 0.04wt%) concentrations, although dramatically high S contents (with a mean value of 52.72wt%). Correspondingly, there are three generations of arsenopyrite: Apy1 (20–50μm) and Apy3 (3–15μm) mainly occur as inclusions in Py1 and Py3, respectively, whereas the latest Apy4 (<5–60μm) can occur either as serrated grains surrounding Py4 or overgrowth Py1 and Py3, or as individual euhedral to sub-euhedral grains. They also contain considerable, but much higher Au contents than pyrite, with the values of 0.6wt%–1.1wt% for Apy1, 0.18wt%–1.32wt% for Apy3 and 0.50wt%–1.75wt% for Apy4, respectively. Besides, they also contain considerable amounts of trace elements such as Co, Zn, Pb, Sb and Se. Arsenopyrite geothermometer constrains the ore-forming temperature responsible for Apy3 formation to 325–385°C. Our result reveals that significant invisible gold accommodated by sulfides is the main cause of refractory ores at the Axi deposit.