A system for non-invasive registration between a patient and a three-dimensional (3D) medical image includes a near infrared 3D camera 110 which extracts a 3D blood vessel image I2 of a patients registration target area during surgical operation; a camera position tracer 120 which traces a position of the near infrared 3D camera 110 and calculates a real world coordinate system of the 3D blood vessel image I2; a controller 130 which extracts a first blood vessel pattern from a 3D medical image I1 of the registration target area, extracts a second blood vessel pattern from the 3D blood vessel image I2, and performs position registration between the patient and the 3D medical image I1 through the extracted first and second blood vessel patterns; and a display 140 which displays a registration result calculated by the controller 130.