Abstract: Vulnerability to sudden service disruptions caused by accidents is one of the major threats in existing logistics systems. This paper focused on capacitated logistics system under accidental disruptions and the two risk mitigation policies were proposed, viz. key facility protection and emergency inventory pre-positioning, to hedges well against accidental disruptions. A fortification planning model for capacitated logistics system was presented in a two-stage stochastic mixed-integer programming framework. The disjunctive decomposition-based branch-and-cut (D²-BAC) algorithm was developed which was used to solve the complicated model. The D²-BAC algorithm was improved by integrating with valid cuts and dynamical 'truncation' strategy of branch-and-bound tree. Extensive computational results confirmed the computational performance of the proposed method and the feasibility of the risk mitigation policies.