With the development of unmanned ships, their use in production is becoming more and more common. However, the unmanned ship work cycle is long and the work environment is complex, and it is still very difficult to calculate the phased mission reliability without unmanned ship. We analyze the unmanned ship phased mission reliability based on the binary decision diagram. Moreover, redundancy is used as the unmanned ship reliability optimization scheme. Considering the resource limitation, and the capacity of unmanned ship, the redundancy allocation scheme of unmanned ship is established. The redundancy allocation scheme is solved by marginal optimization algorithm. Finally, a case study is established to analyze the effectiveness and practicality of the proposed method.