Existing seismic facies analysis schemes, including traditional seismic facies analysis, seismic slice analysis, and automatic classification of seismic facies, can reconstruct the sedimentary systems of basins; however, they are not ideal for basins with few boreholes and many rock types. Herein, we propose a new method for reconstructing sedimentary systems using seismic data, considering the Xisha Trough Basin in the Northern South China Sea as the research object to demonstrate the principles, methods, and technologies of this novel scheme. Based on the six commonly used seismic parameters, three additional seismic parameters (smoothness, neatness, and special waveform) and one geological marker (provenance) were added to improve the recognition of lithofacies. The scanned seismic interpretation technique was used to describe the distribution of sandstone and other skeleton lithofacies; sedimentary environments were determined according to the coastline, shelf break line, and slope toe line; flow path systems were determined according to the paleotopography, incised valleys, and sandstone distribution; and the sedimentary systems of the trough basin were reconstructed through the superposition of skeleton lithofacies, depositional environments, and flow paths. Results show that the sedimentary system reconstructed using the new method contains three elements, namely, lithofacies, the environment, and flow path, which fully reflect the concept of the sedimentary system defined by Fisher and McGowen (1967) ; this overcomes the inherent defects of previous schemes, such as poor lithofacies recognition and the uncertainty of types and boundaries of sedimentary bodies. This method enabled identifying subdivided seismic lithofacies directly from seismic profiles and enhanced the ability to obtain sedimentary information from seismic data. The proposed reconstruction method can be used in areas without boreholes or with many rock types and is significant for marine geology research and oil and gas exploration conducted in the deep sea.