Neuropathic pain (NeP) is a most intractable health problem due to its unsatisfactory treatment effect. Emodin, a natural anthraquinone derivative extracted from Rheum palmatum and Polygonam cuspidatum, exhibits the analgesic effects in various NeP models. However, the underlying mechanisms remain elusive. This study employed whole transcriptome sequencing and metabolomics to elucidate emodin's analgesic mechanism in the spinal cord of chronic constriction injury (CCI) rats. Fifteen-day emodin treatment reversed hyperalgesia and deficit of sciatic nerve function induced by CCI and significantly decreased the concentrations of TNF-α, IL- 1β, IL- 6, IL- 18, and BDNF in the spinal cord of the CCI rats. Transcriptome sequencing revealed altered expression of 85 mRNAs in the spinal cord of emodin-treated and CCI rats, with 53 mRNAs upregulated and 32 mRNAs downregulated. Notably, seven genes (P2RX4, CXCL10, ALOX5, SCN4 A, AURKB, AQP9) overlapped with established NeP targets. Untargeted metabolomic analyses identified 67 significantly altered metabolites (46 upregulated, 32 downregulated) in the spinal cord upon emodin treatment. Integrative analysis highlighted shared pathways between differentially expressed genes and metabolites, including arachidonic acid metabolism, cAMP signaling pathway, and Fc epsilon RI signaling pathway. Western blot and immunofluorescent staining further proved the decreased expression of IBA1, P2X4R, p38 MAPK, p-p38 MAPK, NF-κB, p-NF-κB, and TNF-α, IL- 1β. In conclusion, this study demonstrated that emodin played the analgesic effect in the CCI rats, possibly through suppression of P2X4 purinoceptor signaling in spinal microglia, suggesting a potential therapeutic target for NeP.