Benzethonium chloride (BZC) and methylparaben (MeP) are commonly added into cosmetics as preservatives, which are frequently detected in wastewater treatment plants. Different response patterns of denitrification system were proposed under single and combined exposure to BZC and MeP (0, 0.5, 5 mg/L) by evaluating system performance, functional genes, extracellular polymeric substance (EPS), cytotoxicity, microbial community structure and resistance genes (RGs). The inhibition effect of BZC on denitrification system was stronger than MeP, and the co-exposure of BZC and MeP showed synergistic effect, enhancing the inhibition effect of BZC single exposure. BZC and/or MeP could promote the diffusion of RGs in sludge, including intracellular RGs (si-RGs) and extracellular RGs (se-RGs). Moreover, the single exposure of BZC and co-exposure of BZC and MeP increased the dissemination risks of RGs in water (w-RGs). IntI1 and tnpA-04, mobile genetic elements (MGEs), correlated positively with diverse RGs from different fractions. Notably, the spread of RGs through horizontal gene transfer mediated by MGEs and the flow of si-RGs into extracellular and water were observed in this study.