Systems are the way that nature and society exist, and the system of higher education is the subsystem of the education system. Based on the background of “The Two Overall Situations”, the purpose of higher education’s high-quality development is to build the harmonious relationships between the structure and the function of the higher education, and follow the rules of evolution and control. This paper tries to obverse the higher education with the holistic and global view under the theory of scientific systems, and proposes innovative initiatives for promoting high-quality development of higher education.