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As Missile Flight Control System (MFCS) is a typical complex and high reliable system, its safety and reliability has been turn into an all-important problem. MFCS is frequently employed high level of redundancy for achieving high level of reliability. Dynamic redundancy employed in MFCS can realize complex fault and error diagnosis, recovery and reconfiguration. It is very difficult to analyze the reliability of MFCS by traditional Fault Tree Analysis (FTA) methods. This paper analyzes the weakness of FTA and induces a method of Hybrid FTA that combine dynamic fault tree. Accordingly, static FTA uses binary decision diagrams and dynamic FTA uses Markov Chains. At last, an example is proposed to prove academic analysis.