Abstract: The present disclosure provides a compound function prediction method based on a neural network and a connectivity map (CMAP) algorithm. The compound function prediction method is used to predict an efficacy of a compound, and the compound function prediction method includes the following steps: constructing a compound molecule—encoding vector neural network; constructing and training an encoding vector—marker gene expression variation deep neural network; constructing and training a marker gene expression level or gene expression variation—whole genome gene expression level or gene expression variation neural network; constructing upregulated and downregulated gene sets of a disease or a phenotype; and evaluating a correlation between the compound and the disease or the phenotype.