This paper analyzes the operation process of ship’s entering and leaving port through singlefairway in coastal container terminals and puts forward that the idea of improving the fairway throughput capacity by building anchorages when channel resources are limited. Moreover, a simulation model of ship navigation operation system is built in coastal container terminals considering the inner harbor anchorage. The results show that the number of anchorage and fairway capacity is correlated with an extreme of inner anchorage. Otherwise, it is available to increase the fairway throughput capacity by constructing anchorage in harbor. However, fairway throughput capacity no longer increases when the number of anchorage in harbor exceeds the extreme value. The extreme value could be regarded as the reference number of the anchorage in harbor.