A method combining Department of Defense Architecture Framework (DODAF) 2.0 and Bayesian networks (BN) is introduced. This method can not only provide qualitative description for large systems using DODAF models, but also analyze mission reliability quantitatively based on Bayesian networks. The steps are given to build DODAF-BN models and a missile defense system (MDS) DODAF-BN model is built. Furthermore, the mission reliability of MDS is calculated and analyzed under several scenarios.