With the increasing intensity of ship missions, the mission reliability requirements of various ship systems are getting higher. Especially the new reconfigurable ship electronic information systems, which have the characteristics of resource sharing and reuse, function reconfiguration on demand, software and hardware loose coupling, and business integration, etc., is difficult to be taken into account by traditional reliability design and analysis methods. Therefore, it is imperative to design a reliability modeling and analysis method with careful consideration and strong applicability. Taking the new reconfigurable ship electronic information system as the research subject, this paper firstly adopts the architecture analysis and design language (AADL) to establish a reliability model from three perspectives, namely, system structure, system behavior, and failure impact; then, a model of mission reliability allocation under multiple constraints is developed and solved using the hybrid algorithm of Slime Mode Optimization Differential Evolution (SMA-DE) based on the optimal allocation model of reliability; next, a method for analyzing the mission reliability of ship electronic information systems based on the Goal Oriented (GO) method is proposed, and based on the state probability algorithm therein, a correction algorithm oriented to the co-causal failure modes is derived to realize the quantitative calculation of the mission reliability of ship electronic information systems; finally, an application validation was performed in conjunction with a typical ship electronic information system task. The results show that the method proposed in this study can successfully achieve the mission reliability allocation as well as quantitative analysis of reconfigurable ship electronic information systems under multi-mission requirements.