Rare-earth elements (REEs) are often highly concentrated in sedimentary phosphate deposits, and the microdistribution characteristics and occurrence state of rare earth in these deposits play a crucial role in the overall development and utilization of mineral resources. This study aims to analyze the microdistribution of REEs in REE-bearing phosphate deposits in the Zhijin region of Guizhou at the microstructural level and investigate their occurrence modes. Specifically, rock and mineral identification, X-ray diffraction (XRD), scanning electron microscopy–energy-dispersive X-ray spectroscopy (SEM-EDS), and laser ablation–inductively coupled plasma–mass spectrometry (LA-ICP-MS) were utilized to analyze the samples. The correlation between the distribution of REEs and phosphorus was examined. In addition, the microdistribution of REEs in specific mineral phases and the locations of their occurrence were investigated. The analysis revealed that no REEs existed independently in the deposit. Instead, the distribution of REEs was highly consistent and significantly positively correlated with that of phosphorus. In the microarea structure, REEs were predominantly found both in particles, such as bioclasts, sand debris, and agglomerates, and in phosphate cement, where the main mineral components were collophane and apatite. Conversely, the content of REEs in dolomitized sand debris edges, sparry dolomitic cement, and siliceous cement was considerably lower. Based on these findings, it is speculated that REEs primarily occur within the lattice defects of apatite or on the surface of collophanite. There is a notable contrast in the REE content between the unaltered sand debris at the periphery and the dolomitized sand debris, indicating that the dolomitization in the diagenetic stage resulted in a depletion of REE abundance in the ore. Obviously, the dominant gangue mineral, dolomite, does not serve as the primary host for REEs. Furthermore, the highest concentration of REEs was inside organisms. This finding suggests that the high content of REEs in biological soft tissue may remain under the influence of waves and tides, and REE-bearing apatite may be preferentially separated and fill the cavities of deceased organisms. The second highest content of REEs was found in the shells of organisms, indicating that small shelly organisms absorb phosphorus materials through their life activities to construct their shells, resulting in REE enrichment. Quantitative analysis through sequential extraction procedures displayed that most REEs were present in the residual state, with a smaller portion combined with organic matter. These results confirm that REEs in the Zhijin phosphate deposits primarily exist as isomorphic substitutions in the lattice defects of apatite, with a secondary occurrence as organic matter-bound REEs.