The invention discloses a miRNA-disease association relation prediction method based on similarity and logical matrix decomposition. The method comprises the steps that firstly, the disease function similarity and miRNA function similarity are calculated; then, by utilizing the known miRNA-disease association relation, the disease gaussian kernel similarity and miRNA gaussian kernel similarity areestablished; the disease function similarity and gaussian kernel similarity are integrated to obtain the final disease similarity, and the miRNA function similarity and gaussian kernel similarity areintegrated to obtain the final miRNA similarity. Finally, based on a logical matrix decomposition model, potential characteristic vectors of miRNA and diseases are predicted, and the association relation fraction of the miRNA and disease pairs is calculated according to the logical regression function. According to the miRNA-disease association relation prediction method, the relation of the newmiRNA diseases can also be predicted, the consumed labor, material resources and financial resources in a biochemistry laboratory are avoided, and the accuracy is high.