Carlin-type gold mineralization represents one of the world’s most important Au resources. Despite the many studies conducted in the past three decades, the gold sources and metallogenic dynamics remain enigmatic. Here, we report actively forming auriferous mounds and sulfide concretions from the Middle-Upper Permian basalt-dominated submarine volcanic-sedimentary rocks within the Carlin-style gold deposits, Youjiang basin, China. The volcanic-sedimentary rocks consist of basalt, tuff, scoria, black ash and metalliferous sediments in an unaltered sequence, which overlies the Middle Permian Maokou Formation and underlines by the Upper Permian strata. In this paper, we investigate the native gold nanoparticles in the volcanic-sedimentary rocks, and provide new insight into a new type of Au mineralization in the Youjiang basin. We unravel the mineralogy, trace elements and sulfur isotope compositions of these native gold and associated sulfides (e.g., marcasite and pyrite) via EPMA, in-situ LA-ICP-MS and NanoSIMS analyses. Petrographic obsevations show that native gold grains are present in marcasite microfractures, with sizes of 1 to 5 μm. The marcasites is interpreted to be of sedimentary exhalative (SEDEX) origin, as they are hosted by sulfide concretions comprising of sulfide-rich aggregates, quartz, barite, and basaltic tuff fragments. The EPMA elemental mapping suggests that the native gold grains have high contents of Hg, Cu, Zn and Sb, an ore elements assemblage common in typical Carlin-type Au mineralization (Au-As-Hg-Sb±Cu±Zn). LA-ICP-MS analysis shows the Au0-bearing marcasite is featured by lower Co/Ni ratios (avg. = 0.12), relatively high Ti (mostly 39–890 ppm, some > 10000 ppm) and low Cu (1–32 ppm), As (1–920 ppm), Zn (0–5 ppm) and Au (0–0.53 ppm) contents. The low Co/Ni ratios and elevated Ti contents suggest that the marcasite was likely sedimentary and/or diagenetic process, which associated with high-Ti Emeishan basalt eruption in Middle-Late Permian. NanoSIMS analysis shows that the marcasite δ 34S varies from 20.30‰ to 34.29‰ (avg. = 25.86‰), indicating that thermochemical sulfate reduction (TSR) may have provided the sulfur under open system for sulfate but close for H2S. Overall, this paper proposed that (1) the Middle-Upper Permian volcanic-sedimentary rocks enriched in Au-Sb-Hg±Cu±Zn probably formed the source-bed for the Carlin-gold mineralization in Yanshanian (~140 Ma); (2) significant amounts of gold can occur in the basalt-dominated SEDEX environment. In addition, the genetic relationship between Emeishan plume and Carlin-type gold mineralization is also discussed in this paper. Based on previous studies, the juvenile lower crust beneath the eastern Emeishan large igneous province (LIP) may have been a potential Au source, and the associated mantle underplating may have contributed to the formation of Carlin-style Au deposits. Therefore, we propose a possible genetic link between the Carlin-type mineralization and Emeishan LIP magmatism in the Youjiang basin. Our findings offer a new exploration target which is unaltered volcanic-sedimentary rocks in the Youjing basin, may have been a source of gold for the large-scale Carlin-style gold mineralization in Yanshanian (~140 Ma), and demonstrate that significant amounts of gold can occur in a basalt-dominated SEDEX environment.