PAHs in a sediment core covering ~120 years from Daya Bay in South China Sea were extracted using Soxhlet and high performance thin layer chromatography, and the compound-specific δ13C were analyzed using gas chromatography–combustion–isotopic ratio mass spectrometry. The concentrations of PAHs ranged from 99.3 to 676 ng g−1, with high molecular weight PAHs as a key component. PAHs’ compound-specific δ13C ranged from −35.02‰ to −16.14‰. The patterns of 16 PAHs, molecular ratios, and compound specific δ13C compositions indicate important pyrolytic and petrogenic sources: PAHs derived predominantly from pyrogenic sources (including coal and wood incomplete combustion) before the 1960s, while after the 1960s, they derived predominantly from mixed pyrogenic and petrogenic sources (including automotive exhaust emissions, oil spills, and coal and wood incomplete combustion). Our results can provide important insights into organic pollution emissions influenced by human activities and the urbanization of Daya Bay.