Three ecological restoration systems vegetated with Vallisneria natans, containing ceramisite (VC), bio-carrier and ceramisite (BVC) or Fe/C filler, bio-carrier and ceramisite (FBVC) as functional substrates were constructed for black and odorous water restoration. The average ammonia nitrogen (NH4+-N) conversion rate of FBVC (90.51 %) was similar to that of BVC (88.49 %) and significantly higher than that of VC (53.35 %). However, the average total nitrogen (TN) removal rate of FBVC (84.93 %) was much higher than that of BVC (73.02 %) and VC (52.06 %). Additionally, the average COD removal efficiencies for VC, BVC and FBVC were 52.54 %, 71.84 % and 80.59 %, respectively; while they were 69.72 %, 74.79 % and 97.38 % for total phosphorus (TP). High-throughput sequencing revealed that the richness and diversity of autotrophic denitrifying bacteria, such as Pseudomonas, Pseudoxanthomonas, Arenimonas and Hydrogenophaga increased significantly in FBVC, while the plant growth-promoting bacterium Rhodobacter was dominant. Overall, this study demonstrated that a Vallisneria natans based ecological restoration system coupled with Fe/C internal electrolysis (Fe/C-IE) effectively improved the quality of black and odorous water. In addition, the mechanism of nitrogen, phosphorus and carbon removal was proposed.