BACKGROUND: Shuangxia Decoction (SXD), evolved from " Banxia Shumi Decoction", is composed of Pinellia ternata (Thunb.) Makino and Prunella vulgarisl. SXD has been used to treat insomnia and is considered the first traditional Chinese herbal formula developed specifically for the treatment of insomnia. PURPOSE: This study aimed to investigate the mechanism underlying SXD's effects against insomnia using multi-omics technologies. METHODS: Network pharmacology was employed to predict the active components and core targets of SXD in treating insomnia, utilizing 17 active compounds. The pharmacodynamics of SXD were further validated in sleep-deprived mice. UPLC-QE-Orbitrap-MS was utilized to analyze serum metabolomics and hypothalamic tissue metabolomics of the sleep-deprived mice, revealing the biological mechanism of SXD against sleep deprivation. Rosmarinic acid (RA), a representative component of SXD, was selected to further investigate its anti-sleep deprivation mechanism, including intestinal ROS activity assays, intestinal metabolite analysis, serum metabolomics, gut microbiota analysis, and western blotting. RESULTS: Through network pharmacology analysis, three active compounds and four targets were identified as key contributors to the therapeutic effects of SXD on insomnia. In the sleep deprivation (SD) model regulated by SXD, metabolomics studies revealed 28 differential serum metabolites and 20 differential metabolites in hypothalamic tissues. Among these, three shared differential metabolites (Hypoxanthine, Pyrroline hydroxycarboxylic acid, Hydroxyphenyllactic acid) and two critical metabolic pathways (purine metabolism and arginine and proline metabolism) were identified. In the SD model regulated by RA, varying doses of RA effectively reduced SD-induced ROS accumulation in both the small and large intestines. Analysis of RA metabolites in the intestines revealed 57 putative metabolites, most of which were oxidized products. Serum metabolomics analysis of RA against SD showed 58 differential metabolites, with purine metabolism and phenylalanine metabolism pathways being notably involved. Hypoxanthine was identified as a potential marker for clinical sleep deprivation by integrating serum and hypothalamic tissue metabolomics data from SXD and serum metabolomics data from RA. 16S rRNA sequencing demonstrated that SD significantly altered the abundance of eight gut microbiota species. RA exhibited a restorative effect on specific imbalanced gut microbiota, independent of dosage. Western blotting analysis revealed that RA preserved intestinal epithelial integrity by modulating the expression of tight junction proteins, including ZO-1, occludin and claudin. Meanwhile, RA effectively alleviated SD-induced oxidative stress by activating the Nrf2 signaling pathway, promoting nuclear translocation of Nrf2 and increasing the expression of its downstream antioxidant proteins HO-1 and NQO-1 in the small and large intestines. CONCLUSION: Our study demonstrates that SXD has significant efficacy in alleviating SD. RA, as the representative compound of SXD, can eliminate the accumulation of intestines ROS in SD mice and improve gut microbiota imbalance caused by oxidative stress by upregulating tight junction proteins ZO-1, Occludin, and Claudin, and regulating the Nrf2 signaling pathway. Furthermore, hypoxanthine has been identified as a promising and reliable biomarker for SD.