As the sole supporter of anti-TBM operation, the operational effectiveness of ballistic missile defense (BMD) system attracts more and more attention. The operation simulation by using the theory of System Dynamics (SD) is a feasible study method for the anti-TBM operational effectiveness of the ballistic missile defense (BMD) system. The SD model structure of the anti-TBM operational efficiency assessment is given,and the influence relations among the factors are analyzed. The SD model of the anti-TBM operation is built,the model simulation experiment is executed. And the simulation result is analyzed. The modeling example shows that SD for the anti-TBM operational study is feasible and effective.