The global coronavirus disease 2019 (COVID-19) pandemic originating from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has exerted profound damage to millions of lives. Baicalein is a flavonoid that has gotten a lot of attention as a possible SARS-CoV-2 main protease (Mpro) inhibitor because it can fight off many different viruses. We prepared and screened three sets of databases, each containing 2563 baicalein analogues, against Mpro using molecular docking simulation. The data showed that several baicalein analogues exhibited stable binding energies relative to standard baicalein, indicating that they have some selectivity against Mpro. The binding properties of the top three stable analogues from each database were further analyzed with respect to their binding properties, such as binding mode, binding energy, and binding interaction of putative stable ligand confirmations at the target binding site region.