According to the requirements of information security level protection related systems and standards, this paper focuses on the business requirements of the rail transit Integrated Supervisory Control System, and carries out the design of equal protection level 3 program from the aspects of security technology and security management, respectively. In terms of security technology, the three aspects of security protection, security detection and security audit are designed to meet the requirements of network security, host security and application security. In terms of security management, a series of processes, systems, operating procedures, forms and records are sorted out in five aspects, namely, security management system, security management organization, personnel security management, system construction management, and system operation and maintenance management, to satisfy the requirements of information security management, and to provide a similar reference for the information security level protection program of other similar systems.