Deltamethrin (Del) is a widely administered pyrethroid insecticide that is established as a common contaminant of the freshwater environment and can be detected in many freshwater ecosystems even at lower concentrations. In this study, we investigated the changes in brain transcriptome and metabolome of crucian carp after exposure to 0.6 µg/L Del for 28 days. Antioxidant system analysis revealed that Del exposure significantly increases MDA concentration, and the activity of SOD was significantly inhibited in the brain (p < 0.05). Moreover, a total of 70 differential metabolites (DMs) were identified by the liquid chromatography-mass spectrometry (LC-MS/MS) system analysis, including 32 upregulated and 38 downregulated DMs in the DG group. The DMs associated with chronic Del exposure were enriched in steroid hormone biosynthesis, fatty acid metabolism, and glycerophospholipid metabolisms, such as prostaglandin G2, 5-oxoeicosatetraenoic acid, progesterone, androsterone, etiocholanolone, and hydrocortisone. Simultaneously, transcriptomics analysis revealed that chronic Del exposure caused lipid metabolism disorder, endocrine disruption, and proinflammatory immune response by upregulating the pla2g4, cox2, log5, ptgis, lcn, and cbr gene expression. Importantly, the integrative analysis of transcriptomics and metabolomics indicated that the arachidonic acid (AA) metabolism pathway and steroid hormone biosynthesis were decisive pathways in the brain tissue of crucian carp after Del exposure. Further, Del exposure perturbed the tight junction, HIF-1 signaling pathway, and thyroid hormone signaling pathway. Overall, transcriptome and metabolome data in our study offer a new insight to assess the risk of chronic Del exposure in fish brains. Overall design: During a 28-day exposure period,90 fish were divided into two treatment groups, one was a blank control group (CG), and another was an exposure group with 0.6 µg/L Del (DG),