Recent engineering experiences highlight the Ballistic Missile Defense System (BMDS) as a System of Systems (SoS), and traditional probability models were limited in capturing the complex interactions between component systems. A novel approach was proposed to evaluate the effectiveness of the whole BMDS from the aspect of functional interactions, rather than the functions of components. First, Functional Dependency Network Analysis (FDNA) was introduced to build the analysis model through integrating the component systems in multi-layered kill chains of BMDS. The key metrics were proposed to measure the effectiveness from both probability of raid annihilation and system response time. Finally, the application of this method was demonstrated through a case study, and the result shown the holistic characters of BMDS at SoS level. The case shown that FDNA was a promising way to analyze SoS at high level.