Wetlands are the largest natural methane source, but how submerged macrophytes affect methane emission remains controversial. In this study, the impacts of submerged macrophytes on methane fluxes, water purification, and epiphytic microbial community dynamics were investigated in simulated wetlands (with and without Hydrilla verticillata) treated with norfloxacin (NOR) for 24 days. Mean methane fluxes were significantly lower in treatments with Hydrilla verticillata (56.84–90.94 mg/m2/h) than bulks (65.96–113.21 mg/m2/h) (p < 0.05) during the experiment regardless of NOR. The relative conductivity (REC) values, H2O2, and malondialdehyde (MDA) contents increased in plant leaves, while water nutrients removal rates decreased with increasing NOR concentration at the same sampling time. The partial least squares path model analysis revealed that plant physiological indices and water nutrients positively affected methane fluxes (0.72 and 0.49, p < 0.001). According to illumina sequencing results of 16S rRNA and pmoA genes, α-proteobacteria (type II) and γ-proteobacteria (type I) were the dominant methanotroph classes in all epiphytic biofilms. The ratio of type I/type II methanotrophs and pmoA gene abundance in epiphytic biofilm was considerably lower in treatment with 16 mg/L NOR than without it (p < 0.05). pmoA gene abundance was negatively correlated with methane fluxes (p < 0.05). Additionally, the assembly of epiphytic bacterial community was mainly governed by deterministic processes, while stochastic dispersal limitation was the primary assembly process in the epiphytic methanotrophic community under NOR stress. The deterministic process gained more importance with time both in bacterial and methanotrophic community assembly. Network analysis revealed that relationships among bacteria in epiphytic biofilms weakened with time but associations among methanotrophic members were enhanced under NOR stress over time. It could be concluded that submerged macrophytes-epiphytic biofilms symbiotic system exhibited potential prospects to reduce methane emissions from wetlands under reasonable management.