Phosphogypsum (PG) is a solid waste generated during the production of wet -process phosphoric acid. The silicon and phosphorus impurities in PG greatly affect its resource utilization. In this study, these impurities were removed at atmospheric pressure using a two-step gradient method that simultaneously converted the calcium sulfate dihydrate (CaSO4·2H2O) phase to anhydrous calcium sulfate (CaSO4). Firstly, the SiO2 impurities were extracted and removed by adding a silane coupling agent (KH590) and tributyl phosphate (TPB). Then, the desilicated PG was subjected to phase transformation in a dilute mixed solution of H2SO4-NaCl, during which the co-crystalline phosphorus encapsulated in the gypsum lattice was fully dissolved. Bulk CaSO4 with complete crystalline morphology was obtained after this gradient impurity removal and crystal transformation treatment, and the SiO2 content, P content, and whiteness under optimal treatment conditions were 0.11%, 0.04%, and 92.5%, respectively. Mechanistic study revealed that the key to efficient SiO2 removal is hydrophobic modification of the SiO2 surface by KH590, which improves the extraction rate of SiO2 by TPB. Also, the phase transformation from PG to anhydrous CaSO4 plays a dominant role in the deep removal of P. The phase transformation rate and crystal morphology of PG were further enhanced by adding edetate disodium (EDTA-2Na) as a coordination agent. Moreover, dissolution of phosphorus was promoted in the phase transformation process of dissolution-recrystallization. This work provides practical bases for the disposal and resource recycling of industrial by-product gypsum.