The invention discloses a computer medicine screening method based on a BFGS algorithm. The method comprises the following steps of 1) database establishment, wherein a data set cluster composed of 30,000-40,000 marine micromolecules is subjected to searching loop matching to form a micromolecule library with the similarity of 0-1; 2) database pre-processing, wherein micromolecule conformations, with the similarity of 1, in the micromolecule library obtained in step 1) are deleted; 3) molecular docking, wherein ligands are placed at active loci of a receptor, so that multiple ligands and one receptor are in molecular docking; 4) searching for conformations, wherein the BFGS algorithm is used for searching for the conformations, and when newly-generated conformations are identical to initial conformations or preset difference values of the newly-generated conformations and the initial conformations are smaller than or equal to 0.0001, searching for the conformations is stopped. According to the computer medicine screening method, by optimizing the algorithm, the time of searching for the low-energy conformations of the ligands and the receptor which are combined at the active loci of the receptor in the algorithm is shortened, and the effect and efficiency of virtual screening of a micromolecule database based on the method are improved.