A simulation technique is very useful method to analyze the performance on various engineering area. To automate port systems, we have need of simulation to analyze an effect of assigning and operating devices. Thus we propose simulation methodology to be applied to an analysis, evaluation, planning for port automation. To do this, we have adopted the discrete event system specification based system entity structure / model base framework for modeling and simulation environment. We have performed modeling and simulation on entities of port systems such as container crane, yard tractor, transfer crane, etc. The proposed methodology has an advantage being able to effectively simulate on alternatives of composition and operation strategy for port systems. Some case studies will show the validity of proposed simulation methodology.