Severe contaminations of perfluoroalkanesulfonic acids (PFSAs) existed in the natural groundwater beneath a fluorochemical industrial park (FIP) in Fuxin of China. In the present study, systematic researches were performed to determine the best conditions of efficient treatment for 1 mg L−1 of PFSAs in the synthetic groundwater samples with the periodically reverse electrocoagulation (PREC) using the Al–Zn electrodes. Based upon the orthogonal experiments, the removal efficiencies of perfluorobutane sulfonate (PFBS), perfluorohexane sulfonate (PFHxS), and perfluorooctane sulfonate (PFOS) could reach 87.4%, 95.6%, and 100%, respectively, within the initial 10 min, under the optimal conditions of voltage at 12.0 V, pH at 7.0, and stirring speed at 400 rpm. In addition, the optimized PREC technique was further applied to remove the PFSA contaminations from the natural groundwater samples of the Fuxin FIP, subsequently generating the removal efficiencies of three target PFSA analytes in the range between 59.0% and 100% at 60 min. Moreover, the SEM-EDS analyses showed the hydroxide flocs formed during the process of PREC treatment had clear characteristics of floc aggregates, with the major constituents of O, Al, C, N, Zn, and F elements. As a result, long-chain PFHxS and PFOS tended to be eliminated completely from the natural groundwater by their absorptions on the Al–Zn hydroxide flocs, potentially because of their higher hydrophobicity compared with short-chain PFBS.