To elucidate the patterns of metabolite accumulation in the fruiting bodies and cultured mycelia of Collybia nuda and evaluate the potential of the cultured mycelia as a substitute for the fruiting bodies in terms of active components and antioxidant activity, the mature fruiting bodies and the mycelia cultured for 10, 20, and 30 days were examined for contents of major active components, and the in vitro antioxidant activities of the aqueous and 70% ethanol extracts of the fruiting bodies and mycelia were assessed. Additionally, metabolite profiles were analyzed using non-targeted metabolomics. The results indicated that the contents of total triterpenoids in the mycelia significantly surpassed that in the fruiting bodies. The contents of total flavonoids and total phenols increased with culture time, reaching levels that did not significantly differ from those of the fruiting bodies on the 30th day. The contents of total polysaccharides in the 30-day-old mycelium was significantly higher than in the fruiting bodies. The free radical scavenging capacity of the mycelia were ranked in the decreasing order of hydroxyl radicals > superoxide anion radicals > 1,1-diphenyl-2-picrylhydrazyl (DPPH) radicals. The superoxide anion radical scavenging rate of the mycelium aqueous extract on the 10th day of fermentation was (64.73 ± 1.68)%, while the hydroxyl radical scavenging rate of the ethanol extract was (76.71 ± 1.19)%, demonstrating strong antioxidant activity. Non-targeted metabolomics analysis identified 517 and 450 metabolites as significantly different between the fruiting bodies and the mycelia of different ages and between the mycelia of different ages, respectively. These were primarily classified as lipids and lipid-like molecules, organic heterocyclic compounds, and organic acids and derivatives. K-means clustering revealed time-dependent dynamic changes in differential metabolites from the mycelia during the culture period. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that some differential metabolites were significantly enriched in the basic metabolic pathways and the ATP-binding cassette (ABC) transporter pathway, which were key pathways related to the metabolic differences between the fruiting bodies and the mycelia. In the early stage of culture, the differential metabolites in the mycelia were mainly enriched in the biosynthesis of amino acids, carbon metabolism, and various antibiotic biosynthesis pathways. In the mid-to-late stages, they were significantly enriched in propionate metabolism, biosynthesis of various secondary metabolites, fatty acid biosynthesis, and the pentose phosphate pathway. Additionally, bioactive metabolites such as ergothioneine, dehydroevodiamine and panaxacol were significantly up-regulated in the late culture stage, reflecting a metabolic shift from basal metabolism toward bioactive compound accumulation and metabolic homeostasis. This study provides a theoretical foundation for understanding the metabolic mechanisms of the fruiting bodies and mycelium of C. nuda and for exploiting their high-value bioactive constituents.