The Guangxi-Yunnan-Guizhou district, also named Dian-Qian-Gui “Golden Triangle”, in Southwest China has a large amount of Carlin-type Au deposits. Gaolong is one source of Carlin-type Au deposit in the northwestern Guangxi Province. Pyrites are the major Au-bearing sulfides. Majority of Au are structurally bound Au+, with a few nanoparticles (Au0) occurring in the sulfides. In this study, in situ chemical and S isotopes of pyrites in the Gaolong Au deposit were analyzed by laser ablation inductively-coupled plasma mass spectrometry and laser ablation multi-collector inductively-coupled plasma mass spectrometry, respectively. Backscattered electron (BSE) images and chemical composition analysis showed that the pyrites were divided into four main types: (1) As-poor Py1 (pre-ore sedimentary or diagenetic stage, with prominent spotted and aggregate structures. These are fine-grained pyrite aggregates with rough surfaces and low brightness under the BSE, with edges often eroded by hydrothermal fluid); (2) As-weak Py2 (early ore stage, the core of the rim pyrite, with good crystallization and characteristic corrosion spots in the particle, and with the edge dissolved to show irregular structure); (3) As-rich Py3 (main ore stage, the narrow pyrite rims overgrowing Py1 and Py2, irregularly-shaped and less than 50 μm in width); and (4) As-rich Py4 (fine-grained pyrite, with good crystallization, high brightness, and symbiotic with Py3 and Py1, or an isolated distribution). Py1 contains higher concentrations of S, Fe, and W, and lower Co/Ni ratios (average of 0.91), suggesting a pre-ore origin. The ore-stage pyrites Py2, Py3, and Py4, have elevated mineralization elements—Au of 0.25–72 ppm, As of 2214–40613 ppm, Tl of 0.95–109 ppm, Sb of 31.16–1851 ppm, Cu of 49.09–910 ppm, with average Co/Ni ratios of 0.43. Au was positively correlated with As, Tl, Cu, and Ni in these pyrites. Electron micro probe analyzer (EMPA) elemental mappings show that: 1) Py1 has a low Au content, while Py2, Py3, and Py4 have high Au, As, Cu, Ti, and Mg contents; 2) Au occurs in As-rich pyrite in the form of invisible gold; 3) Rim pyrite contains high concentrations of Cu, which has a good positive correlation with As, while As and Au are decoupled on a smaller scale. The Au contents and Au/As ratios show that the Au-carrying fluids are unsaturated with Au. In situ S isotopes show that the δ34S values range from 10.19‰ to 13.79‰ with a mean value of 12.07‰ for Py1, 8.60‰ to 10.78‰ with a mean value of 9.77‰ for Py2, 1.42‰ to 8.29‰ with a mean value of 6.81‰ for Py3, and − 0.49‰ to 4.42‰ with a mean value of 1.67‰ for Py4. The δ34S data decreased from Py1 to Py4, whereas the As content increased significantly. This indicates that Au and As are enriched in ore-forming fluids, and the ore-forming fluids have low S isotope values. Based on a comprehensive study of geological and geochemical data, we believe that the magmatic hydrothermal genetic model can explain the genesis of the Gaolong gold deposit. We conclude that the S isotope of pyrites resulted from the mixing of magmatic S and sedimentary S, and the Au-bearing fluid came from deep-concealed granite, establishing a magma genesis of the Gaolong Au deposit.