There are more than 50 large-scale berths planned in the long-term of the northern waters of Zhoushan. The low port entry speed，long duration，specific tide，and berthing time windows are the key factors impacting the port navigation efficiency of large ships. Under the conditions of existing and short-term and long-term planned ports，based on the Arena simulation modeling method，a simulation model of large ships in and out of the port in the northern Zhoushan waters is constructed to quantitatively analyze the impact of large-scale berth planning at different stages on the navigation efficiency of ships. The results show that after the short-term and long-term planning，the flow of large ships will increase by 33% and 65% ，and the average waiting time of ships in the Huangze operation area will increase by about 10.5 hours compared with the current situation and that in the Xiaoyangshan operation area and the Molanghu operation area will increase by about 0.5 h and 2 h respectively，which has a limited impact on the overall navigation efficiency.