In a container terminal planning stage，a design value of annual throughput capacity usually can be got according to the formula to calculate.Design and the actual gap of throughput capacity is large，due to the instability and imbalance of the time，the size，the deadweight，the loading and unloading volume of vessels to the port and so on.Taking a container terminal as an example，a handling system macro simulation model of container terminal is established by using computer simulation software FlexSim.Considering the influence of berthing annual capacity and yard storage capacity for the annual throughput capacity of a whole container terminal，its evaluation indexes are displayed.Based on the analysis of the simulation data of the terminal，the evaluation value of annual throughput capacity of the container terminal is 2.6 million TEU.The reasonable assessment of container terminal’s annual capacity can provide a scientific basis for terminal management decision-making and improve the service level of the terminal.