Fault tolerance designs are essential techniques for systems that require high levels of reliability, such as aircraft or spacecraft control system. Imperfect Fault Coverage (IFC) may lead to the failure of a system or subsystem even with adequate redundancy. Previous studies of IFC mostly concentrated on evaluating Coverage Factor (CF), whereas the system failure behaviors with IFC have rarely been involved. Failures that occur in low-layer may be covered by high-layer. However, if the coverage is imperfect, uncovered failure will have functional and physical impact on the system behavior. In this thesis, the failure behavior and reliability of IFC of multi-layer systems are studied and a Binary Decision Diagram (BDD)-based modeling and simu-lation method are proposed to evaluate system reliability. As a case, the failure behavior of an aero engine electronic controller with IFC is studied. The results show that the IFC may impact system behavior without taking the IFC into account, the system maintenance intervals may reduce, and thus the maintenance costs will increase.