Antibiotics and antibiotic resistance genes (ARGs) are severe refractory pollutants in water. However, the effect of an intermittent electrical stimulation on the removal of antibiotics and ARGs from saline wastewater remains unclear. An anaerobic-aerobic-coupled upflow bioelectrochemical reactors (AO-UBERs) was used to treat tetracyclines (TCs) and quinolones (QNs) in saline wastewater. In an aerobic cathode-anaerobic anode reactor at an intermittent voltage of 0.9 V, antibiotic wastewater with a salinity of 15 g/L was treated. The removal rates of oxytetracycline, tetracycline, norfloxacin, and ciprofloxacin were 29.30%, 35.14%, 15.49%, and 15.84% higher, respectively, than those in reactors without voltage application. Compared with non-saline wastewater, the removal of TCs and QNs from saline wastewater was improved significantly by intermittent electrical stimulation. The contribution of the anaerobic region was significantly higher than that of the aerobic region. Intermittent electrical stimulation enriches and degrades Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Dysgonomonas, Hydrogenophaga, Terrimonas, and Methyloversatilis related functional microorganisms. The anaerobic anode reactor with an aerobic cathode was advantageous for the removal of ARGs in general. However, it showed enrichment for certain targeted genes. Therefore, AO-UBERs is an effective method for antibiotic removal. However, its effect on the removal of ARGs needs further investigation.