The South China Sea (SCS) is a crucial region for studying atmospheric aerosols, given its unique geographical location and the interaction of various natural and anthropogenic sources. In this study, we measured the isotopic characteristics of sulfate and nitrate in PM2.5 and utilized a Bayesian isotope mixing model (SIAR) to analyze their sources and formation pathways. Sulfur isotopic values in sulfate (δ34S-SO42−) were 8.7 ± 1.8‰, while nitrogen and oxygen isotopic values in nitrate (δ15N-NO3− and δ18O-NO3−) were −0.9 ± 2.4‰ and 52.3 ± 7.3‰, respectively. The results revealed that sulfate was primarily influenced by marine biogenic sulfur emissions (mostly dimethyl sulfide, DMS), fossil fuel combustion, and biomass burning. Nitrate formation was dominated by the NO2 + •OH pathway (accounting for 69.8–85.7%), with significant contributions from vehicle emissions, biomass burning, and lightning. These findings offer key insights into the complex interactions between natural and anthropogenic aerosol sources in the SCS, contributing to a broader understanding of marine aerosol chemistry.