The remote region of the South China Sea (SCS), situated far from urban mainland areas, is commonly perceived to experience minimal pollution. However, this may evolve into a considerably polluted region owing to increasing anthropogenic pollutants. In this study, we employ a multidisciplinary approach to analyze the surface sediments collected from the offshore area of the southern SCS. Our aim is to explore potential anthropogenic pollutants, their interactions, and the related controlling factors. This research endeavors to enhance our understanding of the current pollution status in the SCS and help making relevant policy management decisions. Comparison with previous reports reveals that now, the area is more extensively and increasingly contaminated by petroleum hydrocarbons and heavy metals (Cd and As) than before. For the first time, we report the recognition of coprostanol and long-chain alkyl mid-chain ketones, unveiling the noticeable incorporation of sewage fecal matter and biomass burning into offshore sediments. Moreover, sedimentary multipollutants (except ketones) exhibit strong correlations with terrestrial elements and fine-sized particles, displaying a roughly high-west/low-east spatial variability in pollutant accumulation or enrichment. These signatures evidently demonstrate the major impact of river discharges (e.g., the Mekong River to the west and the Pearl and Red Rivers to the north) on the SCS. They have hydrodynamic effects on the subsequent basin-wide dispersal of pollutants, driven by monsoon-induced large- and regional-scale currents. The different behavior of burning-related ketones may be partly due to their aerosol form, leading to atmospheric transportation. Because anthropogenic multipollutants pose compounded threats, exacerbating oceanic warming and acidification to marine ecosystems such as the widespread coral reefs in the southern SCS, scientific management of urban emissions is required to mitigate ecosystem degradation in the Anthropocene era.