To reduce the data-hidden issue for multi-beam data of underwater scour region, a new model-dimension adjustment algorithm was introduced, in which the regional isolation and data chromatography threshold adjustment was combined, and the postprocessing method was also provided. Casestudy indicates that this new approach can improve the imaging performance for multi-beam bathymetry surveying data 3 to 5 times. Therefore, the hidden phenomenon of underwater scour datafor hydraulic structures is solved.