In recently years, an increasing number of quaternary ammonium compounds (QACs) enter waster wastewater treatment plants (WWTPs), and coexist with the environmental antibiotics in WWTPs. In this study, dodecyl trimethyl ammonium chloride (ATMAC-C12), dodecyl benzyl dimethyl ammonium chloride (BAC-C12) and didodecyl dimethyl ammonium chloride (DADMAC-C12) were added to nitrifying system treating sewage containing environmental concentration of ciprofloxacin (CIP) (0.2 mg/L), respectively, to explore the different responses of resistance genes (RGs) under the co-occurrence of different kinds of QACs and CIP in nitrifying system. Results showed that partial nitrification was achieved by QACs and CIP co-loading, and the co-occurrence of ATMAC-C12 and CIP had more serious inhibitory in the ammonia oxidation activity, functional genes, extracellular polymeric substances (EPS), and bacterial community structures than BAC-C12 and DADMAC-C12 in nitrifying system. Moreover, the co-occurrence of ATMAC-C12 and CIP stimulated the proliferation of more intracellular RGs in sludge (si-RGs), while more extracellular RGs in sludge (se-RGs) and RGs in water (w-RGs) were enriched under the co-occurrence of DADMAC-C12 and CIP. Mobile genetic elements (MGEs) cooperated with bacteria to alter the profiles of RGs. Partial least-squares path model further confirmed that MGEs had positive effects on the proliferation and transmission of si/se/w-RGs (λ = 0.647, 0.918 and 0.627), and EPS had a most important effect (λ = 1.163) on the w-RGs under the co-occurrence of QACs and CIP. Therefore, it should pay attentions to the consumptions of QACs, and avoid the proliferation and transmission of RGs caused by the co-occurrence of QACs and environmental antibiotics.