The automated analysis technique has gradually replaced the traditional optical observation method in the geoscience fields. However, mineral phase maps obtained from these newer approaches are overly dependent on transforming from elemental to mineralogical compositions. And then, the important pieces of information are destroyed with a complete description of the origin and history of mineral materials. Therefore, using appropriate detection means to analyze the mineralization and genesis which have important implications for mineral mineralization. Here, through comparison with the Raman Mapping, optical microscope, and TMSCAN integrated mineral analyzer for SEM (TIMA), the distribution characteristics, chemical composition, mineral structure, and crystal orientation are studied of typical aegirine rare earth minerals. The results show monazite grains are mostly euhedral-semieuhedral unequal grain structures and fine particle sizes of 100～500 μm. Some particles were metasomatized by phosphorus solution indicating that the deep monazite minerals formed multi-stage mineralization. Bastnaesite minerals are fine-grained and particles are distributed and wrapped irregularly. Aeschynite minerals aggregate clumps or radial forms in irregular. It has obvious directivity that the formation time is consistent with calcite. The ratio of peak area of P—O symmetric stretching mode (ν1) and P—O symmetric bending vibration mode (ν2) is obtained by Raman Mapping data analysis, in which the different growth orientations phase diagrams were obtained of ［PO4］3- monazite minerals in micro areas. Combined with the light microscopic characteristics of monazite. It is proved that monazite mineral has at least three stages of mineralization. The discovery also provides strong evidence for the multi-stage mineralization of the Bayan Obo deposit. In addition, as a fast image method to judge different growth orientations of phosphate, carbonate, and sulfate minerals. It can provide important evidence for judging the fact of multi-stage mineralization for various mineral types. The application of Raman Mapping technology in mineralogy lays the foundation for mineral occurrence characteristics.