A three-dimensional numerical model was applied to simulate tidal current hydrodynamics around Lianyungang Harbor, China, and further the cross-flow features in approach channel was investigated. Field data were used to validate the numerical model. Simulation results showed that vertical velocity in the approach channel is significantly stratified, and a recirculation flow appears in the bottom layer of the channel during the crossing process. This indicates the actual corresponding cross-flow speed varies with shipping vehicles of different drafts. Hence, when designing the effective width of an approach channel, considerations should be taken carefully. Simulation results also showed the strongest cross-flow occurs at around high tide level period in Lianyungang Harbor. In order to effectively ensure the navigation safety in Lianyungang Harbor, we suggest that in navigation scheduling, small ships should enter the harbor at about 1.0h–2.0h later after high tide level, if have to, the two-way shipping should be avoided.