Instant green tea powder was used as raw material to prepare an instant dark tea via liquid-state fermentation by Eurotium cristatum. To understand how the chemical constituents present in fermented green tea develop during fermentation, samples were collected on different days during fermentation for qualitative analyses by ultra-performance liquid chromatography-Q Exactive Orbitrap/Mass spectrometry. Untargeted metabolomics analyses revealed that the levels of original secondary metabolites in the instant green tea changed significantly from day 3 to day 5 during fermentation. Targeted metabolomics indicated that the levels of galloylated catechins (GCs) and free amino acids (FAAs) significantly decreased, but the nongalloylated catechins (NGCs), alkaloids, thearubigins and theabrownins increased dramatically after fermentation. The changes in the contents of catechins, gallic acid and free amino acids in the instant dark tea samples were positively related to the DPPH radical scavenging activities in vitro, and the phenolic acids and FAAs were positively related to the inhibitory effects towards α-glucosidase. These results showed that fermentation by Eurotium cristatum is critical to the formation of certain qualities of instant dark tea.