Resorcinol bis(diphenylphosphate) (RDP) is an emerging pollutant that has been frequently detected in aquatic environments, although its toxicity is poorly characterized. To understand how RDP affects the neural system, two-month-old zebrafish were exposed to RDP at concentrations of 0.1 and 10 μg/L for 60 days. Following exposure, behavioral assessments were conducted, revealing the emergence of anxiety-like symptoms and memory deficits among the adult fish exposed to RDP, especially at the higher concentration. The increased blood–brain barrier (BBB) permeability (4.67–5.58-fold higher than the control group), reduced expression of tight junction proteins and the rapid brain RDP bioaccumulation (15.63 ± 2.34 ng/g wet weight) indicated the neurotoxicity of RDP. Excess reactive oxygen species synthesis (2.20–2.50-fold) was induced by RDP, leading to mitochondrial dysfunction and decreased production of neurotransmitters in the brain, specifically serotonin (5-HT; 16.3 %) and dopamine (DA; 18.1 %). Metabolomic analysis revealed that the low-toxicity RDP dose up-regulated lipid-related metabolites, while the high-toxicity dose up-regulated arachidonic acid metabolism and disrupted amino acid metabolism, including tryptophan and tyrosine metabolism related to dopaminergic and serotonergic pathways. The dysregulation of genes in various cellular processes was identified by transcriptomics, mainly involved in cell adhesion molecules and gap junctions, and oxidative phosphorylation, which were directly associated with BBB permeability and oxidative stress, respectively. Correlation analysis of microbiome-metabolite-host links built a mechanistic hypothesis for alterations in gut microbiota (Actinobacteriota and Proteobacteria) induced by high-dose RDP leading to the alteration of tryptophan, tyrosine, and arachidonic acid metabolism, decreasing the production of 5-HT and DA through the gut-brain axis. This study provides valuable insights into the mechanism underlying RDP-induced neurotoxicity in zebrafish, which can inform ecological risk assessments.