As a popular data carrier, E-mail is an important tool in campus daily work and study, and account stolen issues are typical threats to the E-mail security. Firstly, a systematic study on the optimal security management of Nanjing Agricultural University self-built E-mail system is carried out in this study, then potential risks, courses, and strategies are discussed. Finally, the comprehensive optimization scheme is given, especially on the discovery and handling of account stolen issues, and a novel account status monitoring method based on automated scripts is proposed in this study. Implementation indicates that the proposed scheme significantly increases both the discovery rate and handling efficiency of account stolen issues, particularly stolen cases and spam mails from domain users are explicitly reduced, meanwhile, the manpower of management is saved and the user experience is improved. It also has a certain reference value in college E-mail system management applications.