Lingzhi is a Ganoderma mushroom species which has a wide range of bioactivities. Analysis of the changes in metabolites during the developmental stages of lingzhi is important to understand the underlying mechanism of its biosynthesis, as well as its bioactivity. It may also provide valuable information for the cultivation efficiency of lingzhi. In this study, mass spectrometry based untargeted metabolomics was carried out to analyze the alteration of metabolites during developmental stages of lingzhi. Eight developmental stages were categorized on the basis of morphological changes; starting from mycelium stage to post-mature stage. GC/MS and LC/MS analyses along with multivariate analysis of lingzhi developmental stages were performed. Amino acids, organic acids, sugars, polyols, fatty acids, fatty alcohols, and some small polar metabolites were extracted as marker metabolites from GC/MS analysis, while, lanostane-type triterpenoids were observed in LC/MS analysis of lingzhi. The marker metabolites from untargeted analysis of lingzhi developmental stages were correlated with the α-glucosidase inhibitory activity. Two metabolites, compounds 34 and 35, were identified as potential contributors of the α-glucosidase inhibitory activity. The current result shows that some metabolites are involved in the developmental process and α-glucosidase inhibitory activity of lingzhi.