For reliability and confidentiality of information security systems, the security engineering methodologies are accepted in many organizations. To improve the effectiveness of security engineering, this paper suggests a security methodology ISEM, which considers both product assurance and production processes, takes advantages in terms of quality and cost. To verify the effectiveness of ISEM, this paper introduces the concepts of quality loss, and compares the development costs and quality losses between ISEM and CC through the development of VPN system.