The water quality of Guanting Reservoir couldn't meet the requirement of the standard for drinking water sources in China from 1997 since its pollution. The present work studied the pollution characteristics of per- and polyfluoroalkyl substances (PFASs) in water and sediments in Guanting Reservoir, 4 tributaries and WWTPs by high-performance liquid chromatography-negative electrospray ionization-tandem mass spectrometry (HPLC/ESI-MS/MS). The sources and risks of the identified PFASs were analyzed. There were 11 PFASs detected in the Guanting Reservoir, the average PFASs concentration was 267.89 ng/L in water and 2.17 ng/g in sediment, respectively, which are higher than those in other water sources within and outside China. Perfluorooctanoic acid (PFOA) was the main pollutant in both water and sediments, and it has potential ecological risk (0.1 < RQ < 1) in both water and sediment samples as well as potential health risk with HR value ranges in 0.25–0.64 in water in Guanting Reservoir. Sanggan River and Yongding River are the main input sources of PFASs pollution, and the direct emission from industrial production and the degradation of precursors have been shown to make a great contribution to the PFASs in Guanting Reservoir. The results suggest that continuous monitoring and integrated risk assessment in Guanting Reservoir catchment and more attention should be paid on the pollution control from Sangan River and Yongding River.