This paper introduces the origin,development and application perspective of complexity science and its research status quo of the application of complexity science to the management in China.It analyses the compl exity characteristics of the system of uni versity and raises a new viewpoint th at university is a special complex giant system.This paper brings forth the a pplication perspective of the theory and method of complexity science to the management of university.This paper highlights the core of the manageme nt of university as a complex system t hat should be the integration of three su bsystems that are decision -making s ubsystem,administration subsyste m and a-cademy subsystem.