To calculate the three dimensional(3D) coordinates of surgical instruments in near infrared binocular positioning system of surgery navigation,the correspondence of lighting points on these instruments should be determined.After the subpixel coordinates of these lighting points on the left and the right of image have been extracted automatically,the line equations of all lighting points are obtained according to the intrinsic and extrinsic parameters.Two lines produced by the same lighting point are intersected with each other,from which the 3D coordinates of these lighting points are computed to satisfy the distance relationship among points on surgical instruments to realize stereo matching.The experiment with 15 lighting points in 5 surgical instruments shows that our proposed method can automatically match the points on surgical instruments,and can be used in positionning and tracking instrument for surgery navigation.