Because of the complexity of the theoretical analysis, and the difficulty of giving the quantitative analysis result for complexly astronautic phased-mission system (PMS), such as the Lunar or Mars exploration plan, a reliability analysis method based PRA of PMS is proposed in this paper. With the combined model based on scenario, and comprehensive analysis of the related assessment data and information, this method can not only give the mission reliability level for PMS, but also analyze the weakness of the mission plan. Besides, we can get the importance rank through uncertainty analysis. This method overcomes the dynamics, dependency and uncertainty analysis difficulty of PMS. All results obtained from this method will support the improvement of the system design and optimizing, trade-off for mission plan. The application effect of lunar exploration mission shows the engineering applicability of this method.