To investigate the effects of aerobic and anaerobic fermentation on tea leaves and to compare the differences between different fermentation modes, the metabolite profiles of pre-fermented tea, anaerobic-fermented tea, and aerobic-fermented tea from the same batch were comprehensively analyzed by quasi-targeted metabolomics. The results showed that the two fermentation modes altered tea metabolites significantly differently based on 1162 identified metabolites. A total of 611 differential metabolites were screened in different fermented teas, of which phenolics were the most critical compounds. Both fermentation modes reduced the levels of phenolic esters/glucosides in tea, accompanied by the accumulation of free phenolic. Notably, aerobic fermentation was more conducive for flavonoid glycosides and phenolic acid esters/glycosides reduction, while anaerobic fermentation better for free phenolic acids enhancement, especially gallic acid and its derivatives. Additionally, potential metabolic pathways of tea phenolics during fermentation were depicted, primarily involving the hydrolysis, methylation, and glycosylation of flavonoids, as well as the hydrolysis, esterification, degradation, and amination of phenolic acids. Furthermore, there were also some differences in the metabolism of amino acids, sugars, organic acids and lipids between the two fermentation modes. This study will advance our insights into the fermentation metabolism of post-fermented tea.