This invention discloses a surgical instrument positioning system and a positioning method thereof. Human body natural feature information data presented by medical images like CT taken before surgery is input to the positioning system first and 3D information is rebuilt. Then, position data of a handheld instrument obtained by an optical sensing element is sent back to the positioning system. Through automatically suggesting or designating point by the positioning system or manually selected feature point by an operator, coordinate relationship between patient position and handheld instrument can be built, so as to solve the problem of influence to a surgeon generated during the surgery by using prior art.本發明揭示一種手術器具定位系統及其定位方法，係將術前拍攝的醫療影像(例如CT)所呈現的人體自然特徵資訊數據先輸入本發明之定位系統，並進行3D資料重建，再將經光感應元件所得手持器具的位置資訊回傳至定位系統。接著，可經由定位系統自動建議特徵點或自動指定特徵點或由操作者手工點選特徵點，以建立病患位置與手持器具的座標關係，解決習知技術對於醫生在手術過程中所產生的影響問題。
