With the extensively use of information system, the security issue of the system increasingly becomes a problem. With the defense structure, biological immune system can efficiently defense and obliterate the foreign pathogens. Based on the current research of biological immune system and information system security architecture, this paper comes up with a feasible method to apply the defense structure of biological immune system to information system security architecture. Summarizing common characteristics between the two systems, which proves the possibility of realizing the defense structure in the information system security architecture and come up with an achievable method to construct the three defensive lines. The realization of risk identification in the information system security architecture is analyzed with DEA which is used to identify the risk in the information system security architecture through the establishment of the roduction frontiers’. A mathematical model of DEA is also developed using MATLAB to accomplish the risk analysis based on a set of real data from a company. Afterwards, this paper solves the problem that the previous studies are largely relying on the traditional safety analysis methods or the common risk assessment tools, which is lacking of effective protection technology to cope with the risk in the external environment and lay a foundation for achieving the bionic function of the information system security architecture.