With its low carbon, cost-effective, and environmentally friendly advantages, the pyrite-based autotrophic denitrification (PAD) system received widespread attention for treating low-C/N nitrogenous wastewater. Altered microbial mutualisms and metabolism pathways profoundly affect the treatment performance of the PAD system. In this study, a pyrite-based electrochemical bioreactor (PEBR) was constructed, and a stable long-term operation was achieved. The NO3--N percentage removal peaked at 94.59 % at a current density (CD) of 600 mA/m(2) (influent NO3--N concentration: 30 mg/L) accompanied by an effluent NH4+-N concentration less than 3 mg/L. Under high CD conditions (> 600 mA/m(2)), the SO42- and NO2--N concentrations were reduced to 150 and 0.5 mg/L, respectively. The improvement in PEBR performance was attributed to the mutualistic effects of dominant genera, like Dechloromonas, Acetobacterium, Desulfovibrio, and Arenimonas. The relative abundances of Desulfovibrio and Acetobacterium increased from 1.27 % and 0.96 % (200 mA/m(2)) to 10.36 % and 6.93 % (600 mA/m(2)), respectively. In addition, the increased secretion of extracellular polymeric substances (EPS) enhanced PEBR's electron transport capacity. Mantel test revealed that under current stimulation, dominant genera (like Acetobacterium, and Desulfovibrio) contributed greatly to denitrification and sulfur metabolism. The network analysis identified species most related to target functional genes, further revealing differences in the roles that microorganisms played in various metabolism pathways. These findings provide some insights into the succession of microbial mutualistic relationships in PEBR and guide the use of current in the practical application of PEBR.