The design of postgraduate training management system is inevitably restricted by the characteristics of university organization, the purpose of the management system, the postgraduate training process rules and the behavior of postgraduate students. To make better design of the management system we should follow the basic principles: the system should meet the characteristics of the graduate study in university, the requirements of the ethical and justice, and at the same time the system should reasonably concern and balance the demand of the postgraduate and be cognized in general. At last, the problems which should be paid attention to with the postgraduate management system innovation are discussed.