The invention provides a visual shaft mounting error calibration method and system applied to a homing head. According to the visual shaft mounting error calibration method and system, by designing quick calibration equipment, a homing platform and the quick calibration equipment are mounted on a homing projectile body, the homing platform is electrified, and the homing platform and an upper computer conduct image displaying and communication; and the rotating angle of the homing platform is adjusted through an operating interface for calibration, the calibrated calibration error is stored ina storage unit of a servo control circuit board, after the system is powered on, the system automatically extract the calibration error compensation value and corrects the calibration error compensation value, the visual shaft mounting error of the homing platform is eliminated, orthogonality is maintained, and precise and quick compensation is achieved.