This work aimed to investigate the migration distribution and recovery of rare earth elements (REEs) of phosphate concentrate in the nitrophosphate process of fertilizer production. The nitrophosphate process was divided into three main stages, namely, acidolysis, frozen crystallization, and ammonia neutralization, to detect REE migration and distribution. By controlling the acidolysis stage parameters (55% HNO3; temperature, 60 °C; acid-to-phosphate concentrate ratio, 1.25; acidolysis time, 120 min), the leaching efficiency of REEs reached (95.4 ± 0.7)%. In the frozen crystallization stage, the crystallization temperature mainly affected the transition and distribution of REEs in the acidolysis liquid. By controlling the frozen crystallization temperature at −2 °C and time at 120 min, (4.49 ± 0.03)% of REEs co-precipitated with Ca(NO3)2·4H2O into the solid phase, and the majority of REEs stayed in the crystalline mother liquor. In the ammonia neutralization stage, the value of pH mainly influenced the extraction efficiency of REEs. By controlling the ammonia neutralization stage parameters (pH, 1.7; neutralization temperature, 60 °C; neutralization time, 180 min), the extraction efficiency of REEs in the crystalline mother liquor reached (87.6 ± 0.7)%. The ammonia neutralized precipitates were characterized by scanning electron microscopy, energy dispersive spectrum, X-ray diffraction, and X-ray photoelectron spectroscopy to verify the presence and forms of REEs. Finally, the HSC6.0 software was used to analyze the thermodynamic reaction process of phosphate concentrate decomposition with nitric acid and ammonia neutralization stage. Results showed that REEs in the form of REEH2PO42+, REENO32+, and REE3+ diffused into the mixed acid solution in the acidolysis and frozen crystallization stages, and REEs were precipitated in the form of REEPO4·nH2O, REEnCam(PO4)(3n+2m)/3, and REEF3 in the ammonia neutralization stage.