The vessel’s flexible berthing and crane’s dynamic scheduling is the main operation and management method of specialized container terminal in current years.According to the characteristics of this method,a simulation model of vessel’s flexible berthing and crane’s dynamic scheduling is built by AutoMod,in which a case study is made on the fourth phase of Shanghai Yangshan Deepwater Port.Through simulation and analysis,we get the evaluation data of the design,which offer reference for the decision-making.