The purified SARS-CoV-2 3CLpro protein was concentrated to 7 mg/mL for crystallization. The protein was incubated 1 h with 10 mM baicalein before crystallization condition screening. Crystals of the complex were obtained at 20 °C by mixing equal volumes of protein-baicalein and a reservoir (16% PEG6000, 100 mM MES, pH 5.8, 3% DMSO) with a hanging-drop vapor diffusion method. Crystals were flash-frozen in liquid nitrogen in the presence of the reservoir solution supplemented with 20% glycerol. X-ray diffraction data were collected at beamline BL18U1 at the Shanghai Synchrotron Radiation Facility [25 ]. The data were processed with HKL3000 software packages [26 (link)]. The complex structure was solved by molecular replacement using the program PHASER [27 (link)] with a search model of PDB code 6LU7. The model was built using Coot [28 (link)] and refined with a simulated annealing protocol implemented in the program PHENIX [29 (link)]. The refined structure was deposited to the Protein Data Bank with the accession code listed in Supplementary Table S1. The complete statistics as well as the quality of the solved structure are also shown in Supplementary Table S1.