The rare earth elements (REEs)‐bearing phosphorite was a potential REE resource, which contained all REEs except polonium, among them lanthanide, cerium, neodymium, and yttrium were especially enriched. REEs mainly occurred in fluorapatite (Fap) and had a high positive correlation with phosphorus content. By adopting a new green environmental fatty acid collector GJBW and through one roughing and one refining reverse flotation process, all REEs were pre‐enriched. The flotation concentrate was further leached with citric acid (CA), and all REEs were further enriched. The results of X‐ray diffractometer (XRD), Fourier transform infrared spectroscopy (FT‐IR), and X‐ray photoelectron spectroscopy (XPS) showed that dolomite (Dolo) was removed and Fap was enriched in phosphorite, the selective enrichment of phosphorus and REEs was realized. Density functional theory (DFT) calculation revealed the mechanism of deep purification of REEs and phosphorus in phosphorite by CA at the micro‐scale. The results showed that the number and strength of bonding between CA and Dolo (104) surface were greater than that between CA and Fap (001) surface, and CA was more easily adsorbed on Dolo (104) surface. Under the same conditions, Dolo in phosphorite was more easily leached by CA, while Fap was further enriched. This process provided a theoretical basis for the comprehensive recovery of REEs and phosphorus from phosphorite.