Security system risk management problems are often solved using scenario analysis methods for risk assessment. This method models various attack scenarios on the system to be defended. Many studies consider the risks of a system with elements isolated from each other. At the same time, it is evident that the system’s structure can significantly affect the final values of the integral risk. This study applies previously obtained research results on the influence of complex system structure on their integral risk on security system design. The article considers how the structure of a security system affects its integral risk. The result of the study is the algorithm to design such systems to minimize costs at the operational stage.