A scanning system having a brightness compensation apparatus and method thereof are described. The brightness compensation apparatus includes a statistics window control unit, a brightness statistics logic unit, and a comparing logic unit. The statistics window control unit sets a statistics window setting area. The brightness statistics logic unit generates the current brightness statistics data corresponding to the current page. The comparing logic unit compares the current brightness statistics data with brightness target value to determine whether the brightness compensation apparatus compensates the brightness of next page based on the comparison result and/or image gain of the current page for adjusting the brightness of the scanning system according to the compared result between the brightness statistic data and the brightness target value.