Objective To conduct a metabolic analysis of the intracellular metabolism in baicalein-treated Candida albicans, so as to search for possible biomarkers and to discuss the mechanism of baicalein. Methods GC-MS analysis was used to obtain the metabolic fingerprint of C. albicans before and after treatment with baicalein, and multivariate statistical analysis was used to identify the differences in intracellular metabolites between the treated and control groups, so as to search for the possible biomarkers and discuss the possible relevant metabolic pathways. Results and conclusion Twenty metabolites were screened out and selected as potential biomarkers, and they were primarily involved in oxidative stress, citrate cycle, lipid metabolism and amino acid metabolism.