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A pyrrhotite and sulfur-circulating packed bed reactor (PS-CPBR) was constructed to study the removal process and mechanism of NO₃⁻-N and PO₄³⁻-P with different electron donors. The results showed that the NO₃⁻-N and PO₄³⁻-P removal performance of mixed electron donors (pyrrhotite and sulfur) was superior to the single electron donor (pyrrhotite). The optimum conditions of NO₃⁻-N and PO₄³⁻-P removal in the PS-CPBR were a hydraulic retention time (HRT) of 12 h and a C/N of 0, and the average removal efficiency was 100% and 86.39%. The sulfur in mixed electron donors was able to promote the dissolution of pyrrhotite and the formation of polysulfide to increase the effectiveness of electron donors, promoting the removal of NO₃⁻-N, while the PO₄³⁻-P was removed in the form of FePO₄ precipitation. Microbial and functional gene analyses demonstrated that different electron donors were able to influence the abundance of microbial communities and denitrification functional genes. Meanwhile, mixed electron donors were able to increase the protein content of biofilms and reduce the resistance of electron transfer between microorganisms and electrons.