Large-scale distributed systems, with thousands or even millions of nodes, produce complex and dynamic behaviors. Packet-level simulation is necessary to test and analyze these systems, such as grids, peer-to-peer (P2P) applications as well as worm and DDoS containment systems. However, the current network simulators are not convenient for application layer simulation. We present the NSME, a visualized parallel simulator that allows researchers to simulate their applications in a large virtual network with most details transparent to them. A hierarchical routing is used to enhance the fidelity of simulation and reduce the memory cost of network construction. A variation of CMB algorithm is implemented for parallel synchronization. We show the functions of NSME by three applications: 1) a self-similar background traffic model, 2) a Slammer worm spreading model, and 3) a P2P live streaming system, which demonstrate its effectiveness for simulating any large-scale distributed applications. The performance tests show that the memory cost of NSME is distinctly lower than NS2 and the parallel efficiency can reach about 60% in any of the above applications.