A confocal scanning laser microscope is presented. Its motion control system is built with the DSP - based motion controller. The system worked on a double CPU structure that includes industrial control computer and motion controller, the system adopt friendly man - machine interface In the design of software. The systems tasks are divided into real - time tasks and no - real - time tasks. The lower computer deals with the real - time tasks such as position control and velocity control and the upper computer is used to deal with the non - real - time tasks. The system structure of con-focal scanning laser microscope and the constitute of motion control system as well as the software is introduced .