The Heihaibei gold deposit, located in the south part of the East Kunlun orogenic belt (EKOB), is a newly discovered gold deposit, with similar tectonic setting and geological characteristics with typical orogenic gold deposits in the orogenic belt. The aim of this study is to enrich the understanding of metallogeny of the orogenic gold deposit in the EKOB by studying the genesis of the Heihaibei gold deposit. Pyrite and arsenopyrite, as the predominant Au-bearing sulfides, were investigated using a combination of laser ablation–inductively coupled plasma–mass spectrometry (LA–ICP–MS) and laser ablation–multi-collector–inductivity coupled plasma–mass spectrometry (LA–MC–ICP–MS) for in situ trace elements and sulfur isotope. The analyses results provided significant information about genesis for gold mineralization. There are two types of smoky quartz–sulfide veins (barren and mineralized) in this deposit. Three types of pyrite based on host rock can be distinguished, including barren smoky quartz–sulfide vein- (Py0), mineralized altered monzogranite- (Py1) and mineralized smoky quartz–sulfide vein-hosted pyrite (Py2, including Py2a and Py2b). Py1 coexists with arsenopyrite. Py2a and Py2b occurs as disseminated crystals and veinlet assemblage, respectively. Petrographic observations and LA–ICP–MS analyses show that invisible gold in pyrite and arsenopyrite occurs dominantly as solid solution (Au+). Co/Ni ratios of pyrite and S–H–O isotopic compositions exhibit that pyrites (Co/Ni > 1, δ34SV-CDT = −5.28 to 5.08‰) hosted by barren smoky quartz–sulfide vein are consistent with a magmatic origin, whereas those (Co/Ni < 1, δ34SV-CDT = 7.37 to 9.48‰, δ18OH2O = 3.5 to 4.9‰; δDV-SMOW = −97.9‰ to −93.7‰) hosted by mineralized altered monzogranite and mineralized smoky quartz–sulfide vein were derived from a metamorphic source. Combined with regional tectonic evolution, the gold mineralization in the Heihaibei gold deposit may be related to the metamorphism of the regional strata, which was associated with closure of the Paleotethys Ocean during the early Mesozoic. In the following study, we will pay more attention to the metallogenic regularity of orogenic gold deposits in the EKOB.