A multi-axis motor synchronization control system is provided, which may include a plurality of driving axes and the driving axes are coupled to one another; each of the driving axes may include a position loop controller, a velocity loop controller, a motor and a synchronization calibration device. The position loop controller may generate a velocity signal according to a position command. The velocity loop controller may generate a velocity command according to the velocity signal. The motor may operate according to the velocity command. The synchronization calibration device may calculate the average value of the position signal of the motor and the position signals of the motors of the adjacent driving axes, and then feedback the average value to the position loop controller so as to perform the synchronization calibration.