Abstract: Student management system is an important gist for universities to carry out students' management, and is the significant guarantee to safeguard teaching orderliness. However, in the practice, there is some obstruction existing in the process of the system's execution. Analyzing from the legitimacy of new institutionalism of sociology, it reflects that student management system is confronted with legitimacy crisis that it owns the normative legitimacy while lacks the regulative and cultural-cognitive legitimacy.System's legitimacy can be promoted by means of converting the organizational system's idea, regulating organizational system's goals, implementing the participant mechanism and strengthening the system's cultural construction.