The precious metal Au has a wide range of utilization in various fields, and the Au deposits in China are hosted mostly within the West Qinling Orogen and Jiaodong Peninsula. The Laguhe deposit is a newly discovered medium–size Au deposit in the West Qinling Orogen. Previous studies focused mainly on the nature of Au mineralization in this deposit during different exploration stages, so its genesis and ore–forming physico–chemical conditions and processes remain enigmatic. Here, we present major and trace element analyses of Au–bearing pyrite and arsenopyrite from the Laguhe Au deposit, in combination with machine learning to explore its origin and ore–forming processes. The early and late stages of arsenopyrite show As contents of 40.69–46.22 wt% and 39.12–43.22 wt%, respectively, which constrain corresponding ore–forming temperatures at 320–370 °C and 270–340 °C, respectively. The sulfur fugacities in the two stages range from 10–13.2 to 10–8.4. The arsenopyrite has high Co and Ni contents of 0.02–0.28 wt% and 0.02–0.27 wt%, respectively, which suggest that a deep source mafic magmatic water participated in the Au mineralization. The Fe/(S + As) ratios in pyrite vary from 0.838 to 0.869, which indicate that the Laguhe deposit formed at a moderate to deep ore–forming depth (1.5–8.0 km). Most of the Co/Ni ratios (1–5) and the negative correlation (–0.47) between Fe and As contents in pyrite suggest that the ore–forming hydrothermal fluids in the Laguhe deposit were moderately acidic. Based on the heterogeneous Au contents and the lack of correlation between Fe and Au in pyrite and arsenopyrite, most of Au are suggested to likely exist as nanoparticles, with few as lattice Au in pyrite and arsenopyrite. Machine learning results based on the geochemistry of arsenopyrite and pyrite and geochemical features of arsenopyrite and pyrite classified the Laguhe deposit as a Carlin–like type Au deposit. The Au in the Laguhe deposit migrated mainly in the forms of Au(HS)2– and AuH3SiO4 in hydrothermal fluids, which then precipitated as a result of water–rock reaction, fluid immiscibility and fluid boiling at and around plutons and along faults.