Motion controller is the core of control system of automation equipments such as CNC machine tools and advanced robots.In order to ensure the practicability,realtime and stability of the controller,a design scheme of multi axis motion controller with STM32 as the main controller and FPGA as the auxiliary controller was proposed.The hardware circuit design of the motion controller was given,and the Sshape acceleration and deceleration algorithm was integrated into the motion controller,which improved the control accuracy and effectively avoided overshoot,oscillation and other phenomena.The performance of the motion controller was tested on the platform of the threedimensional dispenser.The results show that each axis of the dispenser can move according to the set trajectory,the operation is stable the realtime performance is high,so it has a good application prospect.