Abstract: The Bayan Obo deposit is a world−class polymetallic ore body characterized by complex mineralogy, fine−grained dissemination, and intricate intergrowths among minerals, which pose significant challenges for beneficiation. These complexities result in low rare earth recovery and inefficient utilization of associated metal resources. To improve overall resource utilization, a hydrogen−based mineral phase transformation process was proposed as a pretreatment approach, and a systematic analysis was conducted on the process mineralogy as well as the thermodynamic behavior and phase transformations of major rare earth minerals under a hydrogen atmosphere. The results show that bastnaesite and monazite are the dominant rare earth minerals, with light rare earth elements being predominant. Bastnaesite exhibits a monomer dissociation degree of 11.26%, mainly occurring as irregular grains or fine−grained inclusions within fluorite, hematite, magnetite, and other minerals. Monazite displays a monomer dissociation degree of 17.32% and primarily exists as micro−inclusions intimately intergrown with gangue minerals such as fluorite and quartz. Thermodynamic calculations and phase analyses reveal that bastnaesite decomposes under a hydrogen atmosphere, forming new phases such as CeOF, while monazite remains thermally stable during roasting. The roasting temperature must be controlled below 850 °C to prevent the formation of HF due to reactions between hydrogen and water vapor. The hydrogen−based phase transformation process enables the selective regulation of rare earth mineral behavior, providing a solid foundation for the comprehensive recovery of polymetallic resources.