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The molybdenum-nickel deposits in Shuidong District of Nayong County (Guizhou Province, Southwest China) are found mainly in black shale series of Lower Cambrian Niutitang Formation, which is another Mo-Ni-rich region besides Zunyi District (Guizhou province). Our systematic study on the Mo-Ni deposits in Tangjiaba of Nayong reveals that layered coarse-grained limestones, spherical beaded limestones concretions are hosted at the lower seam of the Mo-Ni deposits. Its strong negative carbon isotope anomaly (the carbon isotope value of the coarse-grained limestones varies from –2.148‰ to 8.223‰) is similar to that in the modern submarine black smoker chimney. The carbon in the coarse-grained limestones from black rock series of Nayong County might be deep source inorganic carbon. The seams, coarse-grained limestones, ore-bearing coarse-grained limestones and the roof and floor of the deposits are characterized by co-variation on the trace element spider diagram, showing good homology. The extraordinary enrichment of Ag, As and Sb resembles hydrothermal sedimentation. Pro-Earth's core elements Se is strongly enriched in Ni-Mo ore-bearing coarse-grained limestones. The ore-bearing rock series has an extremely low Th/U value (0.012–0.19); in the logU-logTh Cartesian Coordinates, the samples of the roof and floor of the deposits and ore-bearing coarse-grained limestones are found in the East Pacific tise; and the samples of coarse-grained limestones are found between the paleo-hydrothermal dedimentary area and the East Pacific tise. The chondrite-normalized rare earth element patterns of the Ni-Mo deposits show LREE enrichment, Ce negative anomaly, and Eu negative anomaly (which is supposed to be influenced by the deep magmatic processes in an extensional environment) resembles the rare earth element distribution patterns of the fluid and its sediments in modern submarine hydrothermal system. It proves that coarse-grained limestones is characterized by typical hydrothermal limestones, being closely related with the genesis of Mo-Ni deposits in Nayong County, which provides new evidence for hydrothermal sedimentary genesis of Mo-Ni deposit and negative carbon anomaly in the basal Cambrian on a global scale.