As the usage of long-chain perfluoroalkyl and polyfluoroalkyl substances (PFASs) may be gradually restricted, short-chain and even ultra-short-chain PFASs have been widely produced and used, which has put forward new requirements for the simultaneous analysis of the above substances. Using solid phase extraction two-fraction elution and ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS), an experimental method was established for the simultaneous analysis of ultrashort-chain, short-chain, and long-chain PFASs and the precursor perfluorohexanesulfonamide (FHxSA) in low-concentration water, such as tap water and bottled water. By optimizing the volume of methanol in the first-fraction elution, the concentration of ammonia in the second-fraction elution, and the concentration of ammonium acetate in the mobile phase, the high recovery and low detection limit (0.01-3 ng/L) were obtained. In addition, this method was used to measure nine tap water samples and six bottled water samples for validation, and the results showed that the concentration of PFASs in bottled water was lower than that in tap water. This study first reported the trifluoroacetic acid concentration in bottled water (6.61 ± 9.60 ng/L), which was lower than that in tap water (1712 ± 174 ng/L). The main substances in tap water and bottled water are both ultrashort-chain PFASs (C2-C3), accounting for more than 50%. There are few reports on the simultaneous analysis of ultrashort-chain, short-chain, and long-chain PFASs (C2-C18) and the precursor FHxSA in low-concentration water samples, and the new method can be further developed for different environmental media.