The aim of the study was to predict and analyze the molecular interactions between the drug target named γ-hemolysin of Staphylococcus aureus and various flavonoid compounds. Binding affinity for the complexes were calculated based on the free binding energies and the number of interactions. The receptor is a bicomponent, β-barrel pore forming toxin associated with several clinical diseases. The cytolytic and hemolytic activity of the toxin and its involvement in the pathogenesis by damaging the host membranes proved γ-hemolysin to be a valid drug target. The 3D structure of γ-hemolysin downloaded from PDB database (PDB ID: 2QK7) was docked with flavonoid compounds having antimicrobial property. The SMILES of the twenty compounds were obtained from NCBI Pubchem Compound database and downloaded PDB files from Corina tool. Drug-like property and drug-likeness of the compounds were checked by Lipinski’s Rule. Molecular docking was done using Autodock 4.0 resulting in binding energies and the docked complexes were analyzed by PyMol which revealed the binding pattern of amino acids of the receptor with the ligands. Docking analysis revealed that the residue SER90 play an important role in binding with the ligands. The binding energy values of the docked complexes ranged between -6.49 to -5.02 kcal moL^-1. A more negative binding energy was found with Ponciretin compound with -6.49 kcal moL^-1. The lower energy indicated that the compound was in stable conformation and had higher affinity towards the receptor. Thus, Ponciretin compound would be a possible drug compound for inhibiting the cytotoxic and hemolytic activity of the toxin.