The invention provides a drug virtual screening system for crystal complexes, including a visualization subsystem, an evaluation toolbox system, an AI model management subsystem, a large-scale sampling subsystem, a virtual screening subsystem and a data log storage subsystem; Starting from the known crystal complexes, through the visualization subsystem, the evaluation toolbox system, the AI model management subsystem, the large-scale sampling subsystem, and the virtual screening system, a batch of candidate compounds that meet the requirements are recommended. Based on this system, the generation of compound libraries is organically combined with subsequent virtual screening. Users can generate a batch of expected compounds as long as they describe the mode of action of the drug on the protein and the requirements that the drug needs to have. The automated system reduces user intervention and increases the efficiency of R&D.