Understanding drug cocrystal formation and its competitive mechanism is important for improving the physicochemical properties of drugs. In this article, the cocrystal formation of polyhydroxy natural products and their competitive mechanisms are discussed through experimental screening and theoretical calculations. The formation conditions and types of cocrystals were determined based on efficient screening experiments of polyhydroxy natural product cocrystals. To investigate the difficulty and stability of cocrystal formation, competitive cocrystal experiments of polyhydroxy natural products were carried out simultaneously. By simulation of the electrostatic potential surface of molecules and the Hirshfeld surface of crystals, the mode of hydrogen bonding within the crystals was determined. The strength of hydrogen bonding was assessed based on the intermolecular interactions and energy framework within the crystal structure. A “substitution model” was constructed based on experimental results and theoretical calculations, which is of great significance for the prediction and design of natural product cocrystals and provides a feasible solution for improving the physicochemical properties of drugs.