Multistage mineralization overprinting is important for the formation of giant hydrothermal gold deposits. The Youjiang basin in SW China has undergone at least three major deformation phases in the Mesozoic, but their relationship with the large-scale gold accumulation in the region remains enigmatic. Here, we study the large Nibao gold deposit (reserve > 70 t Au) in the northern part of the basin, which has both fault-controlled and stratabound orebodies. We identified a pre-ore stage and syn-ore stage including four tectono-hydrothermal (T-H) substages (i.e., T-H stage 1, 2, 3 and 4) for the local mineralization at Nibao. The pre-ore stage is dominated by coarse-grained pyrite coexisting with TiO₂ polymorphs in the Middle-Late Permian basaltic rocks. The T-H substage 1 is characterized in that the sedimentary pyrites are brecciated in bedding-parallel faults. Fluorination and silicification occur in the T-H substage 2, which is re-brecciated at the T-H substage 3 forming the highest gold grade ore in high-angle thrust fault. The T-H substage 4 presents as fault reactivation within minor calcite and pyrite deposition. Mineralogy and in-situ trace element analyses reveal that mineral dissolution and reprecipitation (incl. dolomite, auriferous pyrite and TiO₂ polymorphs) is ubiquitous during the multistage tectono-hydrothermal process, and the continuous alteration overprinting may have promoted gold accumulation. This replacement process of different generations of auriferous pyrite is also recorded by their inherited sulfur isotopes, giving a narrow δ³⁴S (−3.1 to + 2.1 ‰) range. Anatase is the main accessory phase of TiO₂ polymorphs, as identified with LA-ICP-MS trace element and laser Raman spectroscopic analyses. Moreover, the anatase can been divided into two types (type-I and II) based on their texture, alteration and chemistry. The type-I anatase commonly occurring in the stratabound ore is characterized by higher Zr (mean 1,730 ppm), V (mean 1,412 ppm), and Cr (mean 110 ppm) contents than type-II that coexists with zoned pyrite in the fault-controlled ore (mean 26 ppm, 187 ppm, and 38 ppm, respectively). Additionally, W (mean 636 ppm) and Mg (10,021 ppm) in type-II are much higher than type-I ones (mean 135 ppm W and 476 Mg). These features show that the sedimentary-stage Zr-V-Cr-rich type-I anatase was dissolved via fluid metasomatism, and reprecipitated as the hydrothermal-stage W-Mg-rich and Zr-poor anatase, with gold gradually enriched. Besides, the anatase phase of TiO₂ polymorphs also indicates that the Nibao gold deposit was formed under low pressure–temperature condition. Overall, we propose that the Nibao is a Carlin-type gold deposit, dominated by multistage tectono-hydrothermal events.