Abstract: Nowadays, researches on information security mainly focus on practical technologies, and many of them, such as quantum cryptography, intrusion detection, and disaster recovery, have been highly developed and widely used. However, from the theoretical perspective, there is still a lack of systematical theory which can dominate the operation and guide the development of the information security system from a certain level. In this paper, information security system is researched from a new perspective based on general system theory for the purpose of providing a new way to study information security system. Analytic hierarchy process is adopted to analyze the influencing factors of information security system and relationships among the factors themselves. Then, the interaction among some of the factors is studied through a model of differential equations. As the results show, the model in this paper reflects the inner changes of information security system to a certain extent, and plays a guiding role in the development of information security system.