The invention discloses an intraoperative navigation method and system for assisting in surgery. The method comprises the steps of preoperative scanning, establishment of a three-dimensional model, fixation of a first coordinate system reference mark and a second coordinate system reference mark, scanning through a structured light scanner, rough registration, refined registration and completion of the navigation process through a controller and a displayer. Due to the rough registration process, the process of refined registration between a three-dimensional image and a pre-registered region is very short, and registration preparation time before start of surgical navigation can be greatly shortened. Moreover, since two three-dimensional spaces are utilized for refined registration, the probability of errors is extremely low, and the accuracy and reliability of registration between a sick body and the three-dimensional model can be improved apparently; accordingly, the quality of the surgery is improved, and the success rate of the surgery is increased.