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Equipment systems-of-systems (SoS) effectiveness evaluation can provide important reference for construction and optimization of the equipment SoS. After discussing the basic theory and methods of paral el experiments, we depict an SoS effectiveness analysis and evaluation method using paral el expe-riments theory in detail. A case study is carried out which takes the missile defense system as an example. An artificial system of the missile defense system is constructed with the multi-agent modeling method. Then, single factor, multiple factors and defense position deployment computational experiments are carried out and evaluated with the statistical analysis method. Experiment re-sults show that the altitude of the secondary interception missile is not the key factor which affects SoS effectiveness and putting the defense position ahead wil increase defense effectiveness. The case study demonstrates the feasibility of the proposed method.