Ammonia-oxidizing microorganisms (AOMs, archaea (AOA) and bacteria (AOB)) are primarily responsible for the ammoxidation in constructed wetlands (CWs). However, little is known about evaluating the response of AOA and AOB to engineered nanomaterials (ENMs) and quantifying the shift of their contribution to ammoxidation. Herein, we operated a series of CWs exposing to silver nanoparticles (Ag-NPs), single-walled carbon nanotubes (SWCNTs), and polystyrene nano-sized plastics (PS-NPs) with the wastewater-accumulating concentration of ENMs for 180 days. The results showed that the abundance of AOA amoA gene in situ was far lower than that of AOB, while the abundance ratio of AOA to AOB increased by 15 folds after 180-day experiment. Using DNA stable isotope probing (DNA-SIP) experiment, we found that the active AOB microbiota varied substantially but the AOA was more stable across different groups. Furthermore, the co-occurrence analysis proved that ENMs stress increased the negative coexistence pattern of AOA and AOB; predictive functional profiling showed that the ENMs enhanced the functional advantage of AOA by inhibiting AOB (mainly hydroxylamine oxidation process). Finally, the contribution of AOA increased under exposing to SWCNTs (18.35%), PS-NPs (24.92%), and Ag-NPs (32.14%) compared with control group (0.03%) for 180 days. Despite this, AOB was still the primary executant of ammoxidation in CWs. Overall, in our study, the differences in activities and contributions of AOMs were quantified in CWs, and a significantly negative coexistence relationship between AOA and AOB was revealed when exposed to emerging nanomaterials.