Sulfur autotrophic denitrification (SAD) is an economical, rapid, and efficient wastewater denitrification process. In this study, based on previous studies on SAD fillers, permeable reactive barrier technology with a SAD composite filler as a substrate was created to treat the groundwater of rare earth mines. The feasibility of this permeable reactive barrier technology with a SAD composite filler in rare earth mine engineering applications was demonstrated, with a maximum nitrate removal efficiency of 100%, an average nitrate removal efficiency of 92.68% on days 40-47 (the influent water was 100% rare earth mine groundwater), and a low accumulation of nitrite and ammonium. In addition, the reactor had a good removal effect on 16 rare earth elements (La, Ce, Pr, Nd, Sm, Eu, Sc, Y, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu); except for that of Sc, the removal effects were over 98%. Moreover, scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), and Fourier transform infrared spectroscopy (FTIR) confirmed that extracellular polymeric substances (EPSs), especially polysaccharides, had a facilitative effect on the removal of rare earth elements. Furthermore, 16S rRNA gene sequencing demonstrated that Sulfurovum (18.11%), Ferritrophicum (15.55%), Thiobacillus (13.35%), and Sulfurimonas (8.51%) were the main denitrification genera of the reactor. Overall, the results of this study provide a case reference for permeable reactive barrier technologies with SAD composite fillers in rare earth mine engineering applications.