The integrity of shoreline is disrupted by cliffs, posing obstacles to marine surveying and chart mapping, particularly in research related to the cliff section of the sea area. The present study proposes a method to solve this problem. In the proposed method, we first extract the boundary of the cliff to segment the point cloud according to a designed rule, then calculate the centroid coordinates of each point cloud block, followed by the coordinates of side points on both sides of the boundary of each block from the centroid, and finally create a side point cloud projected to the water surface corrected for elevation. The corrected point cloud is considered a point cloud dataset of the innermost shoreline. Combined with a point cloud projected from the boundary of the cliff section to the water surface, we developed a calculation method for the optimal shoreline position. Our experiment proved that the method could effectively extract the shoreline of the study area. Moreover, compared with that of the commonly used shoreline extraction method, the absolute error of the isoline tracking method was very large, up to several meters. However, the proposed method achieved smaller standard deviation and variance (0.1254 and 0.0157, respectively) than the isoline tracking method (0.9837 and 0.9677, respectively).