The liquid generated during the pre-cooking process of Pholiota nameko is frequently considered waste, and its large-scale disposal may pose environmental risks. This study undertook a comparative analysis of the liquid and the fruiting bodies, focusing on their chemical composition, physicochemical properties, and metabolomics. Standard chemical analysis methods were applied to determine the levels of key components (e.g., polysaccharides, proteins, amino acids) and their physicochemical properties. Meanwhile, untargeted metabolomics based on UHPLC-electrospray ionization mass spectrometry/mass spectrometry (UHPLC-ESI-MS/MS) was utilized for systematic metabolite identification and comparison. The results demonstrate that immersing the fruiting bodies in water at 95 °C for 10 min facilitates the transfer of substantial quantities of compounds into the liquid, with approximately 7.99% of polysaccharides, 41.04% of proteins, and 62.96% of polyphenols in the fruiting bodies being transferred. This liquid is abundant in minerals and functional components, exhibits distinctive physicochemical properties, and holds potential as a natural nutritional enhancer, flavor enhancer, and thickener, with pesticide residue levels remaining within safe limits. Metabolomic data revealed that the pre-cooking treatment significantly altered the metabolite profile. Specifically, several compounds were substantially upregulated in the pre-cooking liquid compared to the fruiting bodies: Ethyl isopropyl sulfide (7.96-fold), Vidarabine (7.41-fold), 5-oxoproline (3.92-fold), and Picolinic acid (2.48-fold). These changes are associated with alterations in the metabolism of vitamins, peptides, and nucleic acids. The research establishes a chemical and metabolic basis for the advanced development and application of P. nameko pre-cooking liquid across various sectors, including food, pharmaceuticals, health products, cosmetics, and agricultural fertilizers. This study presents an innovative approach to addressing the environmental discharge challenges associated with this substance.