With the trend of scale extension in coastal bulk cargo port area and the widely adoption of large bulk cargo carriers recently, higher requirements are put forward for both navigation safety and waterway capacity. Safety duration controlling the trailing time between entering-port ships is one of the factors that affect the waterway capacity. Based on Arena-based port navigation operation simulation model, this paper analyses the impact of safety duration on the waterway capacity in different conditions, and the result was applied to real case studies. The simulation results show that safety duration and waterway capacity are negative power correlated, the change of freight traffic direction has little affect on the sensitivity between the two factors, the influence of safety duration on double waterways is more significant while the impact on single-waterway decreases with the increase of navigation duration.