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Nourishing Yin and Moistening Dryness Formula (NYMD) is a functional food known for its ability to nourish Yin and relieve constipation symptoms. However, the specific molecular mechanism by which it improves Yin-deficiency constipation (YC) is not well understood. This study used metabolomics, network pharmacology, and experimental validation to investigate the effect mechanism of NYMD on YC. Metabolomics analysis identified 34 YC-specific metabolites, while HPLC-Q-TOF/MS confirmed 33 major components of NYMD. Network pharmacology predicted that NYMD may regulate the PI3K/AKT signaling pathway in treating YC. Experimental validation through Western Blot and apoptosis assay confirmed that NYMD inhibits colon cell apoptosis through the PI3K/AKT signaling pathway, alleviating YC. Further confirmation was obtained by blocking the pathway using the PI3K inhibitor LY294002. These findings highlight the PI3K/AKT pathway as the primary mechanism of NYMD to improve YC. This study has significant implications for YC treatment, NYMD development, and its comprehensive utilization.