We examined the vertical distribution of per- and polyfluoroalkyl substances (PFASs) and total organic carbon in sediment cores located in Shenzhen Bay area. We investigated the 210Pbex specific activity of the sediments and calculated the flux of PFASs to understand the temporal variation of PFASs in the past 65 years. The results showed that the concentrations of PFASs generally decreased with depth, ranging from 13 to 251 pg/g dw. The highest PFASs detected were perfluorobutanesulfonic acid, perfluorooctanoic acid, and perfluorohexanoic acid, which correspond to raw materials used in fire-fighting foam and food packaging industries. The flux of PFASs in Shenzhen Bay showed varying growth after 1978 when China's GDP entered a rapid growth stage. Our findings suggest that the vertical distribution of PFASs in Shenzhen Bay is fluctuating with the changes in industrial types and economic development, with implications for studying the fate of other persistent pollutants in the oceans.