After analyzing most of the current Graduation Thesis Management Systems, we proposed an intelligent management system which can meet the requirements of the process of most Graduation Thesis Management Systems. In this paper we mainly introduce the design of the functional components and implementation of the system. We developed the system using ASP.NET and SQL Server database and designed user interfaces for the system manager, principal, student, advisor and supervisor. The system supports batch lead-in of teachers and students' information, two-way choice of thesis topics, managements to thesis grades, statistics and export of thesis related information as well as automated analysis to thesis topic's repetition frequency. The system has been used for two years for the management of our school's graduation papers, and it works well. The implementation of the system is benefit for improving the management efficiency of graduation thesis and has realistic meaning to promote the IT application in school.