As an important component of the measurement and control system, control system software influences on the running of the measurement and control system directly. A new method to design the measurement and control system software based on Micro-Kernel architecture was proposed. On the basis of message processing, measurement and control task was turned into a type of plug by a unified message interface, the vertical hierarchy of in measurement and control system software development was replaced by hierarchical structure under measurement and control task of HPFS-HRRN controlled by Micro-Kernel unit. The measurement and control system software was designed by virtual instrument. The experiment results show that this system software has the ability of extension, good flexibility, and strong reliability.