● MnO2/PCL composite material (MPCM) enhances ammonia and nitrate removal in CWs.● The reduction and re-oxidation of MnO2 both facilitate the removal of ammonia.● Mnammox accounts for 17.16%–27.24% of ammonia removal at the height of 0–20 cm.● MPCM promotes the richness of ammonia oxidizers and denitrifiers in CWs.● MPCM significantly decreases N2O emission in CWs.Constructed wetlands (CWs) are widely used to treat secondary effluent. However, simultaneously removing ammonia (NH4+-N) and nitrate (NO3––N) is challenging because of insufficient oxygen and carbon sources. In this study, a novel composite material (MPCM) comprising MnO2 and polycaprolactone was developed as a substrate for CWs to enhance the synchronous removal of NH4+–N and NO3––N. The CWs with a higher MPCM content (H-CW), lower MPCM content (L-CW), and controlled CW (C-CW) exhibited average NH4+–N removal efficiencies of 75.69%, 70.49%, and 52.40%, respectively. The 15N isotope tracking technique showed that NH4+–N removal was attributed to anaerobic ammonia oxidation mediated by MnO2 reduction (Mnammox), which accounted for 17.16%–27.24% of the NH4+–N removal in the composite material layers (0–20 cm) of the H-CW and L-CW. The richness of ammonia oxidizers in the upper layers (40–50 cm) of the H-CW and L-CW further facilitated NH4+–N removal. Moreover, the average total nitrogen (TN) removal efficiencies of the H-CW and L-CW were 1.99 and 1.59 times that of C-CW, respectively, owing to enhanced denitrification by MPCM. Furthermore, N2O emissions were reduced by 81.31% and 70.83% in the H-CW and L-CW, respectively. This study provides an effective approach for improving nitrogen removal and reducing N2O emissions during the treatment of secondary effluent by CWs.