The invention provides a computer-aided screening method for small molecule target nucleic acid aptamers based on a high-performance computing platform, and relates to the technical field of molecular biology. Firstly, analyze the structure of the small molecule target, and then screen in the small molecule compound library. If the matching principle is met, it will be used as the target small molecule target for molecular docking with nucleic acid molecules. If the matching principle is not met, the molecular structure can be constructed. , the small molecule target after molecular structure construction is used as the target small molecule target, and molecular docking is carried out with the nucleic acid molecule. If the docking is successful, the nucleic acid molecule is the primary nucleic acid aptamer, which solves the binding site between the small molecule target and the nucleic acid molecule Small molecular weight, weak affinity, difficulty in grasping nucleic acid molecules, many consumables, small differences in size, mass, and charge properties between the complex formed by the small molecule target and the nucleic acid itself, and the difficulty in separating the two.