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Triclosan (TCS), as a broad-spectrum bactericide, is extensively used in the fine chemical and textile industries. It is recognized as a new type of environmental endocrine disruptor with frequent detection and environmental pollution. However, the toxicity mechanism regarding neurodevelopment and neurobehavior remains unclear. This study is intended to explore the underlying toxic mechanism of TCS based on gut-brain axis. TCS-chronic exposure affected the development of zebrafish, induced feminization, obesity physical signs and abnormal organ index and caused neurobehavioral abnormalities by inhibiting both neurotransmitter acetylcholinesterase and dopamine activity, promoting brain neuron apoptosis and accelerating diencephalic lesions. Meanwhile, TCS-chronic exposure led to gut microbiota dysbiosis and decreased diversity, such as increased pathogenic bacteria and decreased probiotics in adult zebrafish gut, which caused many pathological damages, including partial shedding and ablation of intestinal villi, inflammatory infiltration, thinning of intestinal wall, and increased goblet cell in villus. Based on the communication between intestinal peripheral nerves and CNS, the above histopathological injuries and disorders were well underpinned and illustrated by the changes of biomarkers and the expression of related marker genes in the gut-brain axis. Additionally, short-chain fatty acids (SCFA), as the regulators of intestinal sympathetic nerve activation, are also secreting products of intestinal microflora and play a crucial role in regulating the balance of intestinal flora and protecting intestinal homeostasis. SCFA in low doses can effectively alleviate and rescue the toxic effects under TCS exposure, which evidenced that TCS exerted systemic toxic effects on the gut-brain axis by influencing the composition and diversity of gut flora in zebrafish, and fully demonstrated the interaction effect between intestine and brain. Hence, these findings contribute to the understanding, prevention, and diagnosis of endocrine disrupting diseases caused by environmental pollutants from the perspective of the gut-brain axis, and strengthening the early warning, management and control of TCS pollution.