Phased mission systems are very common in engineering practices. It has been a challenging task to effectively estimate the reliability of phased mission systems. In the paper, a new reliability synthesis method for phased mission systems is proposed for addressing the challenge. Based on the existed reliability block diagram, the hierarchical synthesis framework of the reliability can be built. The reliability synthesis algorithms for the same level and hierarchical level are respectively presented. Component reliability is the input of the reliability synthesis as the lowest level of the framework, which can be obtained by data-driven method or physics of failure method. The reliability estimation method for three lifetime distribution types is given. The effectiveness of the proposed method is testified and demonstrated by a complicated phased mission system.