A reliable, sensitive, and efficient method was developed for routine analysis of perfluorooctane sulfonate (PFOS) and perfluorohexane sulfonate (PFHxS) in various edible crop matrices including cereal (grain), root vegetable (carrot), leafy vegetable (lettuce), and melon vegetable (pumpkin). The target analytes were extracted by ion-pair approach followed by solid-phase extraction clean-up and HPLC-MS/MS. The type of extraction solvent, clean-up cartridge, and the usage of Supelclean graphitized carbon were evaluated to reach an optimized pretreatment procedure. The matrix-matched standard calibrations relative to the isotope-labeled internal standard were used in the developed method to obtain more reliable quantitative results. The average recoveries at four spiked levels (0.5, 10, 25, 50 ng/g) in the diverse matrices ranged from 70.9 to 114.6% with relative standard deviations (RSD) lower than 11.5%. The matrix-dependent method detection limits using the common equipment (HPLC-MS/MS) were between 0.020 and 0.140 ng/g (dw), equivalent to the 3-130 pg/g (fw), corresponding to the sensitivity of superior equipment (e.g., UPLC-MS/MS and HPLC-QTOF-HRMS). Furthermore, the developed method was conferred with the practicality through determination of the analytes in actual crops sampled from several farms in China's Pearl River Delta.