A parallel simulation model for message passing applications on multi-core cluster systems was presented, then a parallel simulator MCPSim (Multi-core Cluster Parallel Simulator) was designed and implemented. MCPSim adopted a three-layer (i.e., Intra-CMP, Inter-CMP, and Inter-Node) message passing model in its functional and timing model. Furthermore, MCPSim implemented a profiling module to obtain message distribution percentage in the three layers. The current research selected several benchmark applications including PRIME,Jacobi3D, NPB IS and HPL to validate MCPSim. Results show that MCPSim is more accurate than BigSim in performance prediction and can be used in the performance analysis of message passing applications on multi-core cluster systems.