Theaflavins (TFs), an important type of tea polyphenols, have demonstrated promising antiviral activity. However, it is challenging to obtain TF monomers from the direct extraction of tea due to the limited contents after fermentation, which hinders further development of TFs. In the present study, one commercial biotransformed theaflavin fraction (CBTF) was utilized to prepare the high-purity TF derivatives. Firstly, the fingerprints obtained through UHPLC-CAD confirmed the consistency across different batches of CBTF, and UHPLC-QTOF-MS analysis revealed the abundance of TFs in CBTF. Subsequent targeted isolation was performed and a total of fifteen TF derivatives were isolated from CBTF, including two undescribed compounds (9 and 15). Their structures were determined via a comprehensive analysis of NMR and HRMS data. The inhibitory activities against 3CLpro of isolated TFs were evaluated and nine compounds exhibited significant inhibition of 3CLpro in a concentration-dependent manner, with IC50 values ranging from 0.26 μM to 8.26 μM. The structure-activity relationship highlighted the importance of the theaflavin scaffold and gallate unit on 3CLpro inhibition.