Rare earths (REs) containing phosphate rock is a potential REs resource. The unclear occurrence mechanism of REs in phosphorite limits its further development and utilization. Fluorapatite (FAP) is the main REs-bearing target mineral in phosphorite, the microscopic mechanism of REs entering FAP still needs to be further studied from the electronic scale. In this paper, the doping mechanism of REs in FAP was studied by experiment combined with GGA+U calculation. The XRD, SEM, and FT-IR characterization results of hydrothermal synthesis products showed that REs (La, Ce, Nd, and Y) entered FAP crystal, and one of every 20 Ca atoms was replaced by a REs atom. The GGA+U calculation indicated that La-O/F, Ce-O/F, Nd-O/F, and Y-O/F were ionic bonds in general, and the bonding strength of La-O/F, Ce-O/F, Nd-O/F, and Y-O/F increased gradually with atomic number. The substitution difference of La, Ce, Nd, and Y was mainly caused by the gain and loss of electrons in f and d orbitals. The substitution mechanism of REs at the characteristic sites of Fap was studied, which provided a theoretical reference for the selective recovery of REs from phosphorus blocks.