Three types of fermented tea (lightly fermented tea, LFT; semi-fermented tea, SFT; and highly fermented tea, HFT) processed from the same tea variety were subjected to submerged fermentation (SmF) using pure Eurotium cristatum. Chemical analysis and untargeted metabolomics showed that the major chemical components of the three tea infusions underwent significant changes, each exhibiting distinct metabolic profiles, with LFT showing the most upregulated metabolites. Antioxidant assays revealed that all three fermented tea infusions exhibited significantly enhanced antioxidant capacity, with 17 bioactive metabolites (e.g., Phloretin, Epicatechin gallate) showing strong correlations with activity. These distinct variations were correlated with the initial chemical composition of the tea infusions, suggesting that the initial chemical profile served as an important influencing factor in the metabolic process of E. cristatum, yet microbial mediation played a dominant role in guiding the direction of fermentation and shaping the final quality characteristics, despite the presence of spontaneous chemical changes in the tea infusion. Further network pharmacology and molecular docking analyses identified 15 potential health-beneficial antioxidant metabolites, most of which were more abundant in LFT. Combined with sensory evaluation results, our results indicated that LFT was most suitable for making functional antioxidant beverages fermented by E. cristatum.