A large scale HLA-based simulation (federation) is composed of a large number of simulation components (federates), which may be developed by different participants and executed at different locations. Byzantine failures, caused by malicious attacks and software/hardware bugs, might happen to federates and propagate in the federation execution. In this paper, a three-phases (i.e., failure detection, failure location, and failure recovery) Byzantine Fault Tolerance (BFT) mechanism is proposed based on the decoupled federate architecture. By combining the replication, check pointing and message logging techniques, some redundant executions of federate replicas are avoided. The BFT mechanism is implemented using both Barrier and No-Barrier federate replication structures. Protocols are also developed to remove the epidemic effect caused by Byzantine failures. As the experiment results show, the BFT mechanism using No-Barrier replication outperforms that using Barrier replication significantly in the case that federate replicas have different runtime performance.