The autotrophic denitrification of coupled sulfur and natural iron ore can remove nitrogen and phosphorus from wastewater with low C/N ratios. However, the low solubility of crystalline Fe limits its bioavailability and P absorption capacity. This study investigated the effects of amorphous Fe in drinking water treatment residue (DWTR) and crystalline Fe in red mud (RM) on nitrogen and phosphorus removal during sulfur autotrophic processes. Two types of S-Fe cross-linked filler particles with three-dimensional mesh structures were obtained by combining sulfur with the DWTR/RM using the hydrogel encapsulation method. Two fixed-bed reactors, sulfur-DWTR autotrophic denitrification (SDAD) and sulfur-RM autotrophic denitrification (SRAD), were constructed and stably operated for 236 d Under a 5–8-h hydraulic retention time, the average NO3−–N, TN, and phosphate removal rates of SDAD and SRAD were 99.04 %, 96.29 %, 94.03 % (SDAD) and 97.33 %, 69.97 %, 82.26 % (SRAD), respectively. It is important to note that fermentative iron-reducing bacteria, specifically Clostridium_sensu_stricto_1, were present in SDAD at an abundance of 58.17 %, but were absent from SRAD. The presence of these bacteria facilitated the reduction of Fe (III) to Fe (II), which led to the complete denitrification of the S-Fe (II) co-electron donor to produce Fe (III), completing the iron cycle in the system. This study proposes an enhancement method for sulfur autotrophic denitrification using an amorphous Fe substrate, providing a new option for the efficient treatment of low-C/N wastewater.