Due to their connotation, the research-oriented universities have decided the trend and the direction of higher education. Therefore, while constructing and developing research-oriented universities, we must be in accordance with their common development principles and tightly adhere to our country's reality. Through building up scientific management system of these universities, we can improve management efficiency as to guarantee the achievement of their goals. Based on above instructive thoughts, this paper constructs the management system of research-oriented universities in China and analyzes its main functions.