Because of the excessive protein species and number of small molecules, the computational complexity of medicine simulation development is enormous. Molecular docking is an important method to study new medicine, so it is very important to improve the efficiency of molecular docking experimental system. The main purpose of molecular docking is to research the interaction and relationship between protein receptors and ligand small molecules. We set up a Hadoop platform and use Hadoop’s powerful parallel computing ability to dock proteins (1ppe and 1uy6) with a number of small ligands with different numbers through simulation experiments. The corresponding adjustment and optimization of the working process are also carried out. Experimental results show that the system can effectively improve the docking efficiency, and has good stability and convenience.