Serum metabolomics reveals the mechanism of Suanzaoren Decoction (SZRD) in ameliorating anxiety-like behaviors in rats. Insomnia was induced by the modified multiple platform method. Compared with the control group, rats subjected to 18-hour daily sleep deprivation for 21 days exhibited significantly increased total locomotor distance and center zone exploration time (P < 0.01), alongside markedly reduced open arm entry time percentage and frequency (P < 0.001), indicating anxiety-like behaviors. SZRD administration significantly decreased locomotor activity and center zone duration (P < 0.01), while increasing open arm entry time and frequency (P < 0.001), thereby alleviating insomnia-associated anxiety. Pathological sections and immunofluorescence results revealed that, compared with the control group, the model group exhibited inflammatory infiltration in the intestinal mucosal epithelial cells, along with significantly decreased mean fluorescence intensities of ZO-1, occludin, and claudin-1 in the colonic tissue, together with increased hepatic lipid accumulation. SZRD ameliorated intestinal and hepatic damage while enhancing tight junction protein expression. GC-MS analysis demonstrated that the significantly reduced levels of acetic acid, propionic acid, isobutyric acid, valeric acid, isovaleric acid, and isocaproic acid in the colonic contents of sleep-deprived rats (P < 0.05) were significantly reversed by SZRD. UPLC-Q-TOF-MS/MS-based serum metabolomics identified 53 differential metabolites in model rats compared to controls; SZRD significantly reversed 36 of these, encompassing amino acids, organic acids, and lipids. KEGG pathway analysis indicated that SZRD primarily modulated phenylalanine, tyrosine and tryptophan biosynthesis, tryptophan metabolism, tyrosine metabolism, and the tricarboxylic acid cycle. These findings demonstrate that SZRD ameliorates intestinal and hepatic inflammatory injury, reduces intestinal permeability, and exerts anti-insomnia and anxiolytic effects primarily through regulating amino acid metabolism and the tricarboxylic acid cycle, providing scientific evidence for elucidating the therapeutic characteristics of SZRD in treating "consumptive disease with restlessness and insomnia". This experiment was approved by the Animal Ethics Committee of Shanxi University of Chinese Medicine (Approval No.: AWE202310391).