As an efficient nitrogen removal process, heterotrophic-sulfur autotrophic denitrification (HSAD) has attracted extensive attention in wastewater treatment. However, the effects of magnetic powder (Fe3O4) on the electron transport activity in HSAD process remain unclear. Therefore, in this study, a heterotrophic-sulfur autotrophic denitrification system was established to remove nitrogen from marine recirculating aquacultural wastewater for evaluating the effects of Fe3O4. At the optimal Fe3O4 concentration of 50 mg/L, the nitrogen removal efficiency reached 100% with lower sulfate accumulation, and the start-up time was shortened. The assays of denitrifying enzymes and electron transport system activity showed that Fe3O4 improved the activities of nitrate and nitrite reductases, and increased the efficiency of electron transport. Microbial community analysis revealed that Fe3O4 enriched heterotrophic denitrifier Thauera and sulfur autotrophic denitrifier Canditatus Thiobios, and thus enhanced denitrification efficiencies. This study demonstrated that Fe3O4 is an efficient denitrification accelerator in HSAD for treating marine recirculating aquacultural wastewater.