The invention relates to the technical field of dental orthodontics, and more specifically, relates to a method for making an orthodontic micro-implant implanting guide plate. The method includes thefollowing steps: S01, scanning an intraoral three-dimensional (3D) image of a patient with an intraoral scanner; S02, shooting a maxillofacial 3D image of the patient with an oral CBCT device; S03, overlapping the 3D images and data obtained in the former two steps; S04, according to the overlapped image and data, designing a micro-implant nail implant position or implant port diameter size, and generating data; S05, introducing the images and data in the step S03 and S04 into a micro-implant implanting guide plate system, and generating a 3D model of the micro-implant implanting guide plate;and S06, introducing the 3D model of the micro-implant implanting guide plate into a 3D printer, and generating the micro-implant implanting guide plate via 3D printing, wherein the generated micro-implant implanting guide plate can be used for designing more reasonable micro-implant nail implanting position.