Abstract: The Southwest Sub-Basin is an important tectonic unit in the South China Sea. Geochemical information preserved in sediments is essential to the understanding of the sedimentary environment of the basin. In this paper, fatty acids in two sediment cores from the Southwest Sub-Basin were analyzed with GC-MS. The results suggest that: ①The n-fatty acids in the sediment columns B3C and B7 show an even-odd distribution pattern dominated by n-C₁₆ and n-C₁₈, sourced from vascular plants, soil materials, plankton, algae, and bacteria, contributed by both the terrestrial plants and marine diatoms. ②The acid compounds in the core sediments of B3C and B7 are dominated by marine sources. The content of total n-fatty acid and terrestrial dominant n-fatty acids (n-C₂₄、n-C₂₆、n-C₂₈), marine-source dominated n-fatty acids (n-C₁₂、n-C₁₄、n-C₁₆) vary slightly in the vertical direction, indicating that the sedimentary environment was rather stable for most of the time. ③Total fatty acids (TFA) and TFA/TOC ratio indicate that the accumulation rate of organic matter in this area is generally low, and the depositional area belongs to a non-transparent zone without hydrothermal activities.