The invention discloses a medical anatomy auxiliary teaching system based on augmented reality, and relates to the field of biomedical engineering. The system consists of intelligent glasses, an anatomy instrument, a teacher control unit, a wireless router, and a medical image scanning device. A three-dimensional virtual model (vessels, muscle and skeleton) is built through the anatomy information obtained by the medical image scanning device and modeling software. The three-dimensional virtual model and a real anatomic site in an operation vision are integrated and stacked, thereby enabling students to see a subcutaneous internal structure. Meanwhile, the system can obtain the precise spatial information of the anatomy instrument relative to the anatomic site, achieves the augmented display of the operation vision, and has three teaching modes: discovery learning, interactive training, examination and evaluation. The system can assist students carry out theory learning before operation, interactive guide in operation and intelligent estimation after operation, enables the anatomy operation to be standard, improves the operation precision, and reduces the training cost.