This study focuses on the inversion of sub-bottom profile (SBP) data in the northern South China Sea using an empirical relationship derived from sediment acoustic data. The sub-bottom profile is primarily utilized for various marine applications, such as geological mapping and resource exploration. In this research, we present a study conducted in the northern slope canyon of the South China Sea. Firstly, we obtained the seabed reflection coefficient from sub-bottom profiles obtained by the autonomous underwater vehicle (AUV) detection system. Secondly, we utilized the acoustic empirical relationship in the northern South China Sea to establish relationship equations between the seabed reflection coefficient and the porosity, density, and average particle size of the sediment at a main frequency of 4 kHz (the AUV shallow profile main frequency). Then, using these equations, we were able to invert the physical parameters such as porosity, density, and average particle size of the seabed surface sediments. Finally, the inverted results are compared and analyzed by using the sediment samples test data. The overall deviation rate of the inverted physical parameters is within the range of ±10% when compared. The inverted results closely match the measured values, accurately reflecting the dynamic changes in the physical properties of seabed surface sediments. Notably, the average grain size is a direct indicator of the sediment particles size with smaller particles found in deeper water. The variation characteristics of sediment physical parameters align well with the variation of sediment types in the canyon, which is consistent with changes in the water depth, topography, and hydrodynamic conditions of the area. This further demonstrates the reliability of the inversion results.