A control system of multi-shaft servo motor 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).