Aquaculture wastewater seriously threatens the human health. In this study, non-poisonous iron was added into constructed wetlands to purify aquaculture wastewater and the wastewater treatment performances of CWs were explored under the treatment conditions of different plant species and different dosages of ferrous ions. The optimal treatment conditions were experimentally determined as follows: 20 mg/L ferrous ions in CWs planted with Canna indica after 7-day operation, the removal efficiencies of TN, TP and COD were respectively 95 ± 1.9%, 77 ± 1.2% and 62 ± 2%. The improvements in the pollutant removal performance depended on biological mechanisms of plants and microorganisms. The optimal dosage of iron ions could adjust enzyme activities and functional amino acids. Specific functional bacteria (Paracoccus detected based on nirK genetic information and Hydrogenophaga detected based on pufM genetic information) were cultured and domesticated by iron ions. The functional bacteria promoted nitrogen and phosphorus removals.