Characterization of perfluorohexane sulfonate (PFHxS) isomers, a chemical proposed for listing under the Stockholm Convention, is important to elucidate its environmental behaviors and sources. Optimized chromatographic separation coupled with monitoring of the characteristic fragments enabled the identification of four mono-substituted and two di-substituted branched PFHxS isomers. The transitions of molecular ions m/z 399 to the fragments m/z 80 (n-), m/z 169 (iso-), m/z 319 (1m-), m/z 80 (2m-), and m/z 180 (3m-) were selected for quantifying the mono-substituted isomers. Method accuracy of the established LC-MS/MS was verified by comparing the results of technical products with those determined by 19F-nuclear magnetic resonance (NMR). The developed method was then used to quantify the isomeric compositions of PFHxS in the perfluorooctane sulfonate (PFOS) industrial products which contained PFHxS as an impurity, as well as in several kinds of water samples, with the limits of detection for all isomers in the range of 4 to 30 pg/L. For the first time, a liquid chromatography-tandem mass spectrometry method was established to separate and quantify the PFHxS isomers. The isomeric profiling of water samples suggested that PFHxS in the waters was mainly due to the direct contamination of PFHxS rather than from PFOS contamination.