Phosphorite-type uranium deposit represents one of the most important occurrences of global uranium resources. A large-scale uranium-bearing phosphorite has been discovered in the Yankong area of Jinsha, Guizhou, demonstrating significant uranium metallogenic potential. However, the co-existence mechanism of phosphorus and uranium in this area remains poorly understood. Therefore, this study selected three sections located near Yankong Subdistrict (Jinsha County, Bijie City), Minxing Subdistrict (Jinsha County, Bijie City), and Panshui Town (Zunyi City). Sixteen uranium-bearing phosphorite samples were systematically collected to conduct whole-rock major, trace, and rare earth element (REE) geochemical analyses, aiming to reconstruct the paleo-sedimentary environment and determine the material sources. Concurrently, to investigate the microscopic occurrence state of uranium within francolite (carbonate-fluorapatite) in the phosphorite, α-track etching, scanning electron microscopy (SEM), and electron probe microanalysis (EPMA) were employed. The results indicate that the samples exhibit high V/(V+Ni), U/Th, Ni/Co and V/Cr ratios, suggesting that the metallogenic period occurred in an extremely anoxic, sulfidic, and strongly reducing environment. The REE partitioning patterns display significant negative Ce anomalies, MREE enrichment, and weak positive Eu anomalies. Combined with the Zn-Ni-Co discrimination diagram, it is inferred that the metallogenic materials originated from a mixture of phosphorus-rich seawater brought by upwelling ocean currents and deep seafloor hydrothermal fluids. Uranium distribution within the francolite is non-uniform and shows a significant positive correlation with phosphorus. Most of the uranium enters the francolite crystal lattice through the isomorphous substitution of U⁴⁺ for Ca²⁺, while a minor portion exists as nanoscale inclusions on the surface of the apatite, achieving phosphorus-uranium co-existence. By studying the metallogenic environment, material sources, and microscopic occurrence states of uranium-bearing phosphorite in the study area, a three-stage metallogenic model consisting of “upwelling synergistic with seafloor hydrothermal injection supplying uranium and phosphorus—hydrothermal convective circulation enrichment—reducing environment precipitation mineralization" for the uranium-phosphorus co-existence deposit in the Yankong area has been established.