Objective: To investigate the functional classification of differentially expressed genes in manganese-poisoned rats and related metabolic pathways, and to provide a reference for the study of the mechanism of manganese poisoning and gene regulation in the prevention and treatment of manganese poisoning. Methods: Six healthy specific pathogen-free male Sprague-Dawley rats were randomly divided into control group and experimental group according to body weight, with 3 rats in each group. Rats in the experimental group were injected intraperitoneally with MnCl₂·4H₂O (25 mg/kg) at 0.2 ml/100 g once every 48 h, and the control group was injected with phosphate-buffered saline at the same dose. After one month of exposure, the rats were anesthetized and then sacrificed by cardiac puncture blood collection. The striatum was isolated on ice, and RNA was extracted to establish a DNA data library. Whole genome sequencing was used to identify the differentially expressed genes in the rats with manganese poisoning. Gene Ontology functional enrichment analysis and pathway enrichment analysis were performed to investigate the possible metabolic pathways in which the differentially expressed genes may participate. Results: A total of 18439 genes were detected in the striatum of rats, and 17 differentially expressed genes were screened out. Among them, 10 genes were up-regulated, and 7 genes were down-regulated. According to gene function analysis, 164 functional branches and 26 metabolic pathways with high gene enrichment were screened out. The genes were enriched in synaptic signaling, signal transduction, etc., especially behavioral function. The metabolic pathways with high gene enrichment were endocytosis pathway, PI3K-Akt pathway, and neuroactive ligand-receptor interaction pathway, in which the PI3K-Akt pathway had enrichment of the same differentially expressed gene (29 517) as the FoxO signaling pathway and mTOR signaling pathway, and the neuroactive ligand-receptor interaction pathway had enrichment of the same differentially expressed gene (24 415) as the glutamatergic synaptic pathway. Conclusion The differentially expressed genes in manganese-poisoned rats may influence the susceptibility to manganese poisoning through the PI3K-Akt pathway, mTOR metabolic pathway, or FoxO metabolic pathway, and may be involved in behavioral changes.