Provided is a protein-ligand docking prediction method based on quantum mechanical scoring. The method includes evaluating a protein-ligand docking structure by using a molecular mechanical energy-based scoring function and reevaluating the protein-ligand docking structure by using a rescoring function obtained by combining a quantum mechanical factor with the molecular mechanical energy-based scoring function. In accordance with the method using the quantum mechanical scoring, it is possible to more accurately carry out modeling than conventional force field-based methods.