The widely adoption of large coastal bulk cargo carriers brings in higher requirements for matched waterway conditions need to be satisfied. Therefore, this paper establishes a simulation model for ships navigation system in coastal import bulk port area to study the impact of First Come First Service (FCFS), Large-tonner-ship Priority Service (LSFS) and Ship Entering and Leaving Port in Cluster (SELC) on waterway capacity. The results show that the relationship between waterway capacity and port service level is exponential for these three rules,and the impact of FCFS and LSFS on waterway capacity is basically the same. SELC improves waterway capacity of larger scale port area with longer travel time in waterway.