Objective To integrate the gene expression profiles of heart disease animal models and patients, systematically characterize the differences in gene expression, screen differentially expressed genes, analyze the similarities and differences of gene expression, and provide a basis for animal experiments and comparative medicine research. Methods Microarray and transcriptome data of heart disease animal models and patients were downloaded from a public database. Data were sorted by species and disease type and stage, standardization and removal of batch effects were performed, data were converted in the available format for the database, and an online database was built. Results The comparative transcriptomics database of heart disease animal models realized global searching and queries of genes and functional pathways, and analysis of gene expression in humans and mice, diseases, tissues, and stages. It also interactively displayed sample expression profiles, visualized gene expression, and facilitated comparative analysis. The database allowed online differential gene mining, enrichment and identification of functional pathways, exploration of the biological processes of susceptibility genes involved in regulation, explanation of the susceptibility mechanism, and online data analysis. Conclusions A comparative transcriptomic database of heart disease animal models was established to provide data resources and online analysis tools to study heart disease.