This paper proposed an MSC-Transformer model based on the Transformer’s neural network, which was applied to seabed sediment classification. The data came from about 2900 km² of seabed area on the northern slope of the South China Sea. Using the submarine backscattering intensity and depth data obtained by the sub-bottom profiler, combined with latitude and longitude information, a seabed dataset of the slope area of the South China Sea was constructed. Moreover, using the MSC-Transformer, the accurate identification and judgment of sediment types such as calcareous bio-silt, calcareous bio-clay silt, silty sand, medium sand and gravel sand were realized. Compared with the conventional deep neural network CNN, RNN, etc., the model shows advantages when applied to the sediment dataset of the shallow sea slope region of the South China Sea. This confirms the feasibility and validity of the model and provides a reliable and accurate tool for seabed sediment classification in the field of marine science. The completeness and accuracy of the dataset and the good performance of the model provide a solid foundation for the scientificalness and practicability of the study.