This study investigated the impact of drying methods on metabolic profiles of Gomphus luteolus, an edible wild fungi valued for its culinary and nutritional properties but limited by rapid post-harvest deterioration. Using untargeted metabolomics, we analyzed non-volatile nutrients and volatile aroma compounds in samples subjected to four drying treatments: Freeze-drying (FD), hot-air-drying (HAD), oven-drying (OD), and sun-drying (SD). Results revealed significant metabolic divergence: FD minimized lipid oxidation and enzymatic degradation, enriching umami amino acids and ω-3 polyunsaturated fatty acids while suppressing undesirable flavors. Conversely, high-temperature methods promoted characteristic mushroom aromas through lipid-derived volatiles and elevated organic acids but caused substantial nutrient losses. Aroma complexity was highest in HAD/OD due to thermally driven reactions, whereas FD preserved baseline profiles. Overall, FD optimized nutrient retention, while thermal treatments enhanced sensory attributes. This work provides molecular-level insights into drying-induced metabolic shifts, establishing a “metabolite-process parameter” framework to guide high-value processing of wild fungi.