In view of the limited through capacity of the artificial long channel in Huanghua coal port area，we study the influence of strict navigation rules for over-limit ships such as LNG ships on navigation efficiency of coal ships. According to the current situation of navigation management，we adopt the multi-agent simulation modeling method to establish a simulation model of ship-channel-berth operation in coal port area，and quantitatively evaluate the influence of the navigation efficiency caused by the over-limit ships entering and leaving the port through the analysis of six working conditions. The results show that when the number of over-limit ships reaches 70 per year，coal ships delay caused by the single over-limit ship will be more than 2.4，and the average delay time is more than 1.1 h. Moreover，the stricter the regulation rules of over-limit ships are，the greater the impact is. It is suggested that the coal port area should strictly regulate the number of over-limit ships to ensure the passing capacity of coal ships.