In order to reduce the complexity of modeling the logistics systems, the tools of HCPN is used. The usage of hierarchy and substitude transition is introduced in this article. We made the quantify and qualitative analysis by the Simulation Performance Report and Message Sequence Chart which get by the monitor of CPN. The monitor not only observe the tokens of place but also the occur frequency of transitons. Not only the correct of the model is guarantied and the good fundament of modularization and hierarchy design for the material flow simulation software architecture is formed.