Phosphogypsum, a solid waste produced in the wet phosphoric acid process, can lead to severe environmental pollution. Recently, the resource utilization of phosphogypsum as a raw material for cement retarders and other products has received widespread attention, but it is limited by the high cost of purifying impurities, such as phosphorus and fluorine, contained in phosphogypsum. Herein, a novel method for purifying phosphorus and fluorine in phosphogypsum by in situ recrystallization was developed and has been employed in industrial application successfully. Further, the purification process parameters and mechanism were investigated based on a series of characterizations. The experimental results indicate that the removal efficiencies of phosphorus and fluorine achieve 86.4% and 95.71% under the optimized conditions, respectively. Significantly, during the recrystallization and washing process of fresh phosphogypsum, CaSO 4 •0.5H 2 O dissolves and then transforms into larger rhombic CaSO 4 •2H 2 O particles. Meanwhile, the impurities, such as water-soluble phosphorus ([H 3 PO 4 , H 2 PO 4 − , HPO 4 2− , and Ca(H 2 PO 4 ) 2 ), eutectic phosphorus (CaHPO 4 •2H 2 O), and water-soluble fluorine (F − , Na 2 SiF 6 , and K 2 SiF 6 ), carried in fresh phosphogypsum are transferred from the solid phase to the liquid phase, thereby achieving purification of phosphogypsum. This research offers robust theoretical backing and practical guidance for the effective purification of phosphogypsum.