In recent years, the BDD (Binary Decision Diagram) approach has been widely used for phased mission system (PMS) reliability analysis. To successfully use BDD technique, a key issue is the variables ordering while converting the fault tree into BDD format. This will impact the finalized BDD size. Compared with the single phase system, the phased mission system is more complex due to the dependency between its phases. So it may not be suitable if using the existed BDD variable ordering approaches for PMS-BDD construction. A new PMS BDD variable ordering method is proposed in this paper. Considering the structure and characteristic of PMS, this new method emphasizes the adjacence of neighbor variables' ordering and simplifies the BDD construction process through common failure components reduction. An example given in the end manifests the advantage of this new method.