Antibiotics and microplastics are prevalent pollutants in mariculture. Consuming contaminated bivalves can potentially endanger human health, but the impact of microplastics on antibiotics bioaccumulation in bivalves and the related health risks to consumer health risks is not fully understood. We obtained bivalves from a mariculture farm and set up exposure scenarios with ciprofloxacin (1μg/L) alone, microplastics (0.6mg/L) alone, or their combination on mussels for 2-weeks. We investigated ciprofloxacin accumulation and analyzed the effects of these pollutants on detoxification and intestinal microbiome changes. Furthermore, potential food safety hazards related to ingestion of antibiotic-tainted bivalves were also assessed. We found that the accumulation of the ciprofloxacin in bivalves was significantly aggravated by the presence of microplastics. There was a significant increase in the production of antioxidant substances in the host's haemolymph, and an enhanced synthesis of antioxidants by the predicted metabolic functions of the intestinal microbiome. Concomitantly, microplastics exacerbated intestinal dysfunction, with a reduction in beneficial Spirochaetes and an increase in pathogenic bacteria Treponema, which may lead to deterioration of detoxification in the host. Additionally, an assessment of human gut health risks was conducted on the residual ciprofloxacin in bivalves combined with human consumption habits. The estimated target hazard quotients and cancer risk were below safety thresholds, directly consuming contaminated bivalves poses little toxicity. However, with raw mussels consumption, the dietary exposure doses of ciprofloxacin to human gut microbiome exceeded minimal selective concentrations for resistance. This could promote the growth of potentially resistant bacteria, indicating a risk of antibiotic resistance.