An origin calibration method of a manipulator is provided. The origin calibration method includes steps of: (a) controlling the manipulator to move in accordance with a movement command, and acquiring the 3D coordinates of the reference anchor points reached by the manipulator; (b) controlling the manipulator to move in accordance with the movement command while an origin of the manipulator being offset, acquiring the 3D coordinates of the actual anchor points reached by the manipulator, and acquiring a Jacobian matrix accordingly; (c) acquiring a deviation of a rotation angle of the manipulator according to the Jacobian matrix, the 3D coordinates of the reference anchor points and the actual anchor points, and acquiring a compensation angle value according to the deviation; and (d) updating the rotation angle of the manipulator according to the compensation angle value so as to update the origin of the manipulator.