Considering that the dyeing wastewater exhibits numerous refractory substances and that poor removal effects on total nitrogen in treatment have great harm to the aquatic environment. Based on that, a novel Fe–C microelectrolysis coupling aerobic granular sludge (AGS) system was developed in continuous-flow, involving Fe–C filter, hydrolysis acidification (HA) and oxidation ditch (OD) with two-zone sedimentation tank (TST) to promote granulation. Herein, AGS could cultivated in OD within 50 days, the biomass concentration and settling ability were further improved (the mixed liquor suspended solids (MLSS) and sludge volume index at 30 min (SVI30) were stable at approximately 6000 mg/L and 27.0 mL/g, respectively). The results showed that Fe–C and HA effectively transformation or removal of some refractory pollutants and improved the biodegradability of wastewater (BOD5/COD from 0.22 to 0.32). The nitrogen removal efficiency improved after granulation, which could reduce from 72.0 mg/L in influent to 22.5 mg/L in effluent (lower than the limit value). Microbial community analyze showed that refractory pollutants transformation microorganisms (Acetobacter etc.) enriched in HA, conventional denitrification microorganisms (Hyphomicrobium etc.), Fe–C related denitrification microorganisms (Unclassified_f__comamonadaceae and Hydrogenophaga) and AGS related denitrification microorganisms (Pseudoxanthomonas etc.) both enriched in OD.