Rare earth elements (REEs) are considered critical elements in modern society due to their irreplaceable role in new innovative and energy technologies. The giant carbonatite-related Bayan Obo deposit contributes most REE resources in the world’s market, while its origin is still unclear because of the complicated and diverse REE ore mineralogy and texture. Thescanning electron mircroscopy SEM)-based automated mineralogy allows for the numeric assessment of rocks and ores’ compositional and textural properties. Here, we use TIMA (TESCAN Integrated Mineral Analyzer) to quantitatively characterize REE ore mineralogy from the deep drill core within the H8 unit (“dolomite marble”) to better understand the deposit. The mineral composition, occurrence, and Ce elemental deportment of the borehole ores at different depths (i.e., 1107 m, 1246 m, 1406 m, 1546 m, and 1682 m) were obtained. The results show that the main types of ores in the investigated samples can be divided into banded REE-Fe ores, banded REE ores, disseminated REE-Fe ores, and veined REE ores. REE and gangue minerals vary significantly in abundance and occurrence. Monazite-(Ce) and bastnäsite-(Ce) are the primary REE host minerals, and both contribute the most to the REE budget. Other REE minerals, such as parisite-(Ce)/synchysite-(Ce), cerite-(Ce), huanghoite-(Ce)/cebaite-(Ce), and aeschynite-(Ce), are significant contributors. The gangue minerals generally include fluorite, barite, magnetite, pyrite, quartz, magnesio-arfvedsonite, and minerals of the biotite and apatite groups, among others. Combined with the newly published mineral-scale chronological and isotopic geochemical analyses, it is reasonable to conclude that the later hydrothermal fluids remobilized and redistributed the original Mesoproterozoic carbonatitic REE minerals and formed a high variable ore mineral assemblage. Furthermore, it is demonstrated that the mineralogical study using TIMA can provide accurate and reliable mineralogy data for the comprehensive interpretation of the complex REE ores, and extend our understanding of the deposit.