For the analysis of perfluorobutane sulfonate (PFBS), perfluorohexane sulfonate (PFHxS) and perfluorooctane sulfonate (PFOS) in shells, an extraction method of mixed inorganic acid digestion coupled with solid phase extraction (SPE) was established. The target compounds were determined by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The shell powder was at first digested with the mixture of nitric acid and hydrochloric acid, then the digestion solution was adjusted to pH 6 with sodium hydroxide, and cleaned up with Oasis WAX SPE cartridge. The perfluoro sulfonated chemicals were quantified with HPLC-MS/MS using electrospray ionization in negative ion mode with internal standard method. The limits of detection (LODs) were of 0.28 ng/g for PFBS, 0.42 ng/g for PFHxS and 0.43 ng/g for PFOS, and matrix recoveries of the perfluoro sulfonated chemicals were 94.88%-96.24%. The analytical results for the shells of two bivalves from Bohai Bay showed this pretreatment method is suitable for the determination of perfluoro sulfonated acids (PFSAs) in shells. Concentrations of PFSAs in the shells ranged from < LOD-0.70 ng/g, which were an order of magnitude lower than those in the soft tissues of these bivalves.