Understanding the process and influencing factors of the oxidation of pyrite is beneficial for the management of environmental problems in mining areas. In this study, we investigated the morphology and geochemistry of the pyrite and related goethite from the weathering crust of the Shangmanggang (SMG) gold deposit, southwest China, via petrographic work, electron microprobe analysis, X-ray diffraction analysis, and PHREEQC geochemical modelling. The weathering profile of the SMG is composed of the unweathered Carlin-type zone, the semi-weathered zone, and the highly weathered red-clay zone, and different types of pyrite, framboidal pyrite (Py1), cube pyrite (Py2), and zoned pyrite (Py3), were differentially oxidized and transferred into corresponding pyrite-pseudomorphic goethite commonly comprised of the early and late phase. Furthermore, the stronger oxidation is related to more late goethite with more Al and Si content. The ubiquitous dolomite buffer kept the pH of the pore fluid neutral, resulting in the precipitation and accumulation of a goethite coating around pyrite, which further reduced the oxidation rate and formed pyrite-pseudomorphic goethite ultimately via coupled dissolution-reprecipitation reactions. In addition, the different mineralogical properties resulted in the differential oxidation of pyrite such that the smaller grains oxidized faster, and As within the pyrite accelerated the oxidation. Moreover, the rate-limited oxidation of pyrite under carbonate buffer prevents acid mine drainage (AMD) from forming and limits As release from arsenian pyrite into the external environment.