Benzylalkyldimethylethyl ammonium compounds (BAC) and polyvinyl chloride microplastics (PVC MPs), as the frequently detected pollutants in wastewater treatment plants (WWTPs), have attracted more concerns on their ecosystem risks. Therefore, this study investigated how the sulfur autotrophic denitrification (SAD) system responded to the single and joint stress of PVC MPs (1, 10 and 100mg/L) and BAC (0.5, 5 and 10mg/L). After 100 days of operation, the presence of 10mg/L BAC led to obviously inhibitory effects on system performance and microbial metabolic activity. And the additions of PVC MPs or/and BAC stimulated the proliferation of intracellular resistance genes (RGs), whereas exposure to BAC increased the abundances of extracellular RGs and free RGs in water more significantly. Compared to the joint stress, BAC single stress resulted in higher abundances of free RGs in water, which further increased the risk of RGs propagation. Moreover, the interaction between mobile genetic elements and extracellular polymeric substances further increased the spread of RGs. Pathogens might be the potential hosts of RGs and enriched in SAD system and plastisphere, thereby leading to more serious ecological risks. This study would broaden the understanding of the environmental hazards posed by PVC MPs and BAC in WWTPs.