The invention is to provide a navigating method and system for drilling operation in spinal surgery. The method and system is applied to the subjects who receive pedicle insertion operation in spinal surgery. The specific vertebras are under radiography using X-ray machine at both anterior/posterior and lateral views. These imaging are then transmitted into a computer system for image distortion correction and registration. By drawing the safety regions of the pedicle on the indicated vertebra in both AP and Lat. images, three-dimensional safety volumes of the pedicle of the vertebra are developed by intersection operation. Therefore, prior to and during the clinical spine operation, surgeons are able to safe navigation by referring the referential orientation via the developed system.