Based on the three-dimensional ocean numerical model (FVCOM) in the theory of finite volume method,we establish the three-dimensional tidal model and convection-diffusion model in shallow waters of Lianyungang.With the advection-diffusion model,we calculate the concentration of the conservative in the main port of Lianyungang port and analyze the three-dimensional water exchange characteristics in the main port.The results show that the water exchange capacity of the entrance is the best and the water exchange capacity decreases from the entrance to the bottom in the main port.Also,the difference of water exchange capacity between the surface and the bottom is very small.The average residence time,semi-exchange time and flushing time of the main port are 13 d,5 d and 84 d respectively.