The Bayan Obo deposit is the largest comprehensive Fe-REE-Nb deposit in the world. The shape of ore bodies and the texture of ore are closely related to ductile structures. To understand the deformation characteristics and evolution of ore structures in the ore district, this study collected rocks for microscopic and Th-Pb geochronological analysis based on macroscopic structural analysis. Results show that rhombic, banded, and folded ore structures can be identified in the Bayan Obo deposit, which reflects gradually strengthening ductile deformation, involving minerals such as magnetite, monazite, fluorite, rare earth minerals, and dolomite. The most widely developed banded structures represent the products of ductile deformation of rocks during the compression stage. Selected syntectonic monazite gives a Th-Pb age of 432 ± 4 Ma, belonging to the Early Paleozoic. Referring to previous geochronological results in the Bayan Obo deposit, it is believed that this age represents the ductile deformation occurs at the Middle Silurian. In addition, the coarse-grained monazite shows an age range of 477 to 838 Ma and the geological significance represented by these ages is not yet clear. It may be related to the alteration of monazite during the mineralization by hydrothermal activity, resulting in a certain degree of lead loss. The U-Pb age of zircon in the undeformed diorite-porphyrite dyke is 274 ± 4 Ma, which constrains the upper limit of ductile deformation. Combining regional geological results, it is suggested that the Middle Silurian ductile deformation in the Bayan Obo deposit corresponds to the collage between the North China plate and the Bainaimiao arc. The intense collision has transformed the original ore-forming structure from both macro- and microscopic aspects, forming the existing pattern.