Diquat is a widely used bipyridyl herbicide, and central nervous system injury (CNSI) is a major cause of death in acute poisoning; early serum markers and underlying mechanisms remain unclear. We prospectively classified acutely poisoned patients into healthy controls (JKDZ), diquat patients without CNSI (NCNSI), patients who developed CNSI during hospitalization (CNSI1), and patients presenting with CNSI (CNSI2). Early serum underwent transcriptomic, proteomic and metabolomic profiling. Multivariate and differential analyses with KEGG/GO enrichment and O2PLS integration identified key pathways and candidate markers, which were evaluated by violin plots and ROC curves. Mechanistic relevance was tested in zebrafish embryos exposed to diquat (Control, 100, 175 mg/L) by assessing developmental toxicity, locomotor behavior and neuroinflammation-related gene expression. Integrated multi-omics clearly separated the four clinical groups and revealed progressive disruption of glycolysis/gluconeogenesis, central carbon and amino-acid metabolism, serotonergic synapse and ferroptosis pathways with increasing CNSI. Integration pointed to early l-histidine depletion, mitochondrial dysfunction and accumulation of the neurotoxic metabolite methylmalonate. Serum 5-hydroxyindoleacetic acid (5-HIAA), BAG1 and CLIC1 strongly discriminated NCNSI from CNSI1/2 (AUC 0.94-1.00). In zebrafish, diquat caused microphthalmia and other malformations, reduced swimming distance and speed, and robust induction of cxclc1c, ifna6, mmp9 and tnfa. In zebrafish, targeted absolute quantification confirmed a dose-dependent decrease in l-histidine and increases in MMA and 5-HIAA following diquat exposure. Clinical multi-omics combined with zebrafish evidence suggests an association between diquat exposure, histidine depletion, mitochondrial stress and methylmalonate accumulation, accompanied by neuroinflammation and CNSI. Serum 5-HIAA, BAG1 and CLIC1 are promising early-warning biomarkers for CNS complications in diquat poisoning.