In this study, the ciprofloxacin (CFC) and copper (Cu) were selected as the target pollutants, indoor culture experiments were designed, and the interaction relationship between microbial communities and antibiotic resistance genes (ARGs)under ciprofloxacin and copper co-contamination in river sediments was explored using high throughput 16S rRNA sequencing and quantitative PCR. The results showed that the ARGs abundance, microbial community composition and functions were significantly different among different experimental groups (CFC contamination, Cu contamination and co-contamination). The total relative abundance of ARGs of each sample showed an increasing trend first, and then it decreased at the end of culture experiment. Co-occurrence network analysis suggested that intI 1 was associated with 3 types of ARGs and 8 bacterial communities, regarded as a bridge between ARGs and microbial community. Meanwhile, the bacteria that belonged to Proteobacteria, Acidobacteria, Firmicutes, Bacteroidetes and Chloroflexi was considered as the potential ARGs hosts in the aquatic environment. Based on the partial redundancy analysis, the microbial community had the highest overall interpretation rate (49.77%) for the change of ARGs abundance among MGEs, microbial communities, pollutants and other factors. At last, the path analysis showed that CFC and Cu pollutants indirectly affect the spread and diffusion of ARGs mainly through microbial communities.