<p>This study inverted the grain size of surface sediments on the seafloor in a route area of the eastern South China Sea based on sub-bottom profile data and discussed the impact of hard seabed and bottom sediment anomalies on the inversion results. The physical properties of seafloor surface sediments, such as grain size, porosity, and density, are important aspects of marine sedimentology research and marine engineering geological analysis. Inverting these physical properties through the Biot-Stoll model is one of the currently used methods. This inversion method requires the extraction of the seafloor reflection coefficient, while the presence of bottom sediment anomalies and hard seabed geomorphology in the study area may affect the accuracy of the extracted seafloor reflection coefficient. However, the impact of these two types of geomorphology on the accuracy of this inversion method is currently lacking in research. The inverted grain size obtained through a series of inversion calculations was compared with the actual measured grain size obtained from sampling, with a relative error of 2.31% to 29.31%. Analysis shows that hard seabed and bottom sediment anomalies affect the accuracy of the seafloor reflection coefficient, leading to larger errors in the inversion results near areas with such geomorphology. Therefore, in areas with hard seabed and bottom sediment anomalies, it may be suitable to use the inversion method of this study with high-resolution data by increasing the density of survey lines and sampling points to reduce errors caused by the impact of geomorphology. In addition, based on the characteristic that the seafloor reflection coefficient is affected in hard seabed and bottom sediment anomaly areas, it may be used as an auxiliary means to identify abnormal seafloor geomorphological areas, providing a reference for engineering disaster geological prevention.</p>