The present invention relates to a control system of multi-shaft servo motor, wherein, comprises a position loop module (400) for receiving a position loop given value and a position feedback value of respective shelves and figuring out a velocity loop given value; a velocity loop module (500) for receiving the velocity loop given value and a velocity feedback value of respective shelves and figuring out a current loop given value; a current loop module (200) for receiving the current loop given value and a current feedback value of respective shelves and outputting a current loop output value; a PWM signal generation module (300) for receiving the current loop output value from the current loop module (200) and generating a PWM signal for controlling respective shelves of the servo motor; and a multi-shaft time sequence control module (700) for controlling the position loop module (400), the velocity loop module (500), the current loop module (200) and the PWM signal generation module to receive and process the signals.