The invention relates to a method and application system for simulating ligand molecule and target receptor reaction based on a computer and calculating and forecasting thermodynamics and kinetics parameters of the reaction. The method mainly comprises the following steps of: designing a method for calculating combined free energy of a ligand molecule and a target receptor, and designing a multi-target molecule docking method and developing an application system of the docking method based on the calculating method; simulating and sampling the interaction mode of the ligand molecule and the target receptor by the system, grading the free energy combination of the ligand molecule and the target receptor, and building a method and system for the potential energy surface of the combined free energy of the ligand molecule and the target receptor according to the simulating and sampling result; building a method and system for identifying a reaction path of the ligand molecule and the target receptor according to the potential energy surface; and determining a active site and a transition site of the reaction to calculate the thermodynamics and kinetics parameters. The method and the system provide important basis and a forecast evaluation method for drug development, and are expected to improve the drug development efficiency and save experimental expenses greatly, thus serving as an effective auxiliary means for the drug development.