Abstract: Submarine pipeline is an important energy lifeline. However, the sandpits occurring along the route of submarine pipeline threaten seriously the in-place stability of the pipeline. In order to assess the impact of the scouring and silting of the sandpits by sea currents in the route area of the submarine pipeline from Shenzhen to Hong Kong on the in-place stability of the pipeline, the issues of the scouring and silting of the sandpits within the pipeline route area are analyzed by comparing long-term measured data and combining with numerical simulation method. The results from the established finite element model are in a good agreement with the measured data. And the law of the scouring and silting of the sandpits under the actions of waves and tidal currents and the variations in the next decade are proposed. That is, the sand mining area is dominated with a silting environment with its northern boundary extending toward northwest and being far away from the direction of the pipeline, indicating no impact on the pipeline, whereas its southern boundary extending toward southeast, which can cause the scouring of the pipeline near the Tonggu Waterway. At the eastern boundary of the sand mining area the slope of the sandpits close to the pipeline has been subjected eroding at its top, thus causing the boundary line of the sandpits expanding towards the pipeline. This study can provide a scientific and effective method for analyzing the scouring and silting of the sandpits by sea currents in the area of the Shenzhen-Hong Kong submarine pipeline route.