Silver nanoparticles (AgNPs) has been widely detected in the substrates of constructed wetlands (CWs), posing threaten to pollutants removal efficiency of CWs. However, the way to alleviate the toxicity of AgNPs on CWs is unclear. In this study, the gravel (GR), biochar (BC), pyrite (PY) and pyrite coupled with biochar matrix (PYBC) were selected as substrates to restore the pollutants removal efficiency of CWs under the exposure to the environment (0.2 mg/L) and accumulation (10 mg/L) concentration of AgNPs. Results showed that the BC and PY showed limited mitigation effects, while the PYBC alleviated the toxicity significantly. Especially in the exposure to the accumulation concentration of AgNPs, the removal of NH₄⁺-N, TN, COD and TP in the PYBC were 10.2%, 8.3%, 9.4% and 10.7% higher than that in the GR, respectively. Mechanism analysis verified that AgNPs were transformed into Ag–Fe–S core shell aggregates (size >200 nm) decreasing bioavailability and the damage to cytomembrane. The PYBC restored the nitrogen removal efficiency by increasing the abundance of Nitrospira and Geothrix, which these bacteria were defined as nitrifiers and Feammox bacteria. This study provides a promising strategy to mitigate AgNPs’ toxicity on the pollutant removal efficiency in CWs.