Typhoon is an important meteorological phenomenon that affects the living and development of human beings on the southern China coast. However, there is still lack of clarity in the paleo-typhoon history and its influence on the evolution of the ancient human settlement environment since the mid-Holocene. Here, we identify six typhoon-like deposits from a core retrieved from the northern South China Sea shelf, close to the Pearl River Estuary, based on accelerated mass spectrometry ¹⁴C dating, grain size, and geochemistry. The sand fractions, CaO, Sr, SiO₂/TiO₂, and SiO₂/Al₂O₃ were used to indicate the typhoon-like deposits. Results show that the ages with high-frequency typhoons are present ~200–300 cal yr BP, ~800–1000 cal yr BP, ~1500–1700 cal yr BP, ~2000–2100 cal yr BP, ~2400–2500 cal yr BP, and ~2700–3000 cal yr BP. Our results are comparable to the records from adjacent regions. Significantly, the vast tides occurred in the duration of ~2700–3000 cal yr BP in southern China, which probably caused the ancestors’ migration to the inland. Further studies are needed to deeply study the paleo-typhoon history in the southern China coast to verify our results.