OBJECTIVE: To explore the therapeutic effects of Zhuyang Tongbian Decoction (ZTD) on vasoactive intestinal peptide (VIP) and 5-hydroxytryptamine receptor (5-HTR) in colon tissues, intestinal flora, and fecal metabolites in mice with functional constipation (FC). METHODS: A total of 36 BALB/c mice were divided into six groups: control, model, positive (Cisapride), and ZTD groups with three dosages (1.5 g/mL, 3 g/mL, and 6 g/mL). All mice, except those in the control group, were induced with FC by gavage using the compound diphenoxylate. After establishing the model, each group received the respective treatments by gavage for two weeks. The laxative effect was evaluated by comparing changes in body weight, fecal weight, fecal water content, and the percentage of carbon powder propulsion in the small intestine. Immunohistochemistry was used to assess the distribution and expression of VIP and 5-HTR in proximal colon tissues. Additionally, 16S rRNA sequencing and liquid chromatography with quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) non-targeted metabolomics analysis were used to examine the effects of ZTD on intestinal flora composition and metabolites in FC mice. RESULTS: ZTD treatment not only alleviated FC symptoms but also increased the number of VIP and 5-HTR-positive cells in colon tissues. Furthermore, ZTD improved the diversity and abundance of intestinal flora, significantly increasing the relative abundance of Prevotellaceae, Bacteroidales_S24-7_group, Ruminococcaceae, and Roseburia while reducing the abundance of Proteobacteria, Desulfovibrionaceae, Rikenellaceae, Porphyromonadaceae, and Erysipelotrichaceae. In terms of metabolites, ZTD significantly elevated the levels of deoxyadenosine and adenine, while significantly lowering the levels of L-leucine, L-threonine, succinate, tyramine, L-tyrosine, and dopamine. CONCLUSIONS: This study provides a theoretical basis for the treatment of FC with ZTD. ZTD increased levels of the intestinal neurotransmitters VIP and 5-HTR and promoted the colonization of beneficial bacteria, including the dominant butyric acid-producing bacterium Roseburia. Additionally, ZTD reduced fecal dopamine levels, indicating its value as a therapeutic approach for FC.