The potential toxicity of BPQDs has received considerable attention due to their increasing use in biomedical applications. In this study, the toxicity of BPQDs at concentrations of 5 μg/mL, 50 μg/mL, and 500 μg/mL on the brain-gut axis was assessed in zebrafish. Following 35 days of exposure, the neurotransmitter, locomotor behavior, gut barrier (physical barrier, chemical barrier, and microbial barrier), and gut content metabolism in zebrafish were evaluated. The results indicated that BPQDs induced the locomotor behavior abnormalities, inhibited acetylcholinesterase activity, induced dopaminase activity, and promoted apoptosis in zebrafish brain tissue. Meanwhile, BPQDs caused damage to the physical and chemical barriers in zebrafish intestinal tissue, which increased the permeability of the intestinal mucosa, and induced oxidative stress and apoptosis. The gut microbiota was analyzed by 16S rRNA gene sequencing. The results showed that BPQDs caused dysbiosis of the gut microbiota, resulting in decreased diversity. Specifically, the relative abundance of Firmicutes, Bacteroidetes, and Actinobacteria decreased, while the relative abundance of Proteobacteria and Clostriobacteria increased. At the genus level, the high concentration BPQDs showed a significant increase in Cetobacterium, Pleisionomas, Aeromonas, and other bacteria. Bioinformatic analysis revealed a correlation between the relative abundance of the gut microbiota and antioxidant levels, immune response, and apoptosis. Statistical analysis of the metabolomic revealed significant perturbations in several metabolic pathways, including amino acid, lipid, nucleotide, and energy metabolism. In addition, correlation analysis between microbiota and metabolism confirmed that gut microbiota dysbiosis was closely associated with metabolic dysfunction. The histopathologic injury supported the changes in biomarkers and the expression of related marker genes in the gut-brain axis, indicating the communication between the gut peripheral nerves and the CNS. The results indicate that BPQDs induce gut microbiota dysbiosis, disrupt metabolic function, and induce neurotoxicity, probably by disrupting the homeostasis of the microbiota-gut-brain axis. In summary, this study demonstrates the effects of BPQDs on physiological changes within the zebrafish brain-gut axis and provides valuable data for assessing the toxicological risks of BPQDs in aquatic ecosystems.