The present invention provides an automatic heart disease detection system based on a convolutional neural network. The automatic heart disease detection system comprises a database, a lesion information processing module, a key frame extraction module, a data cleaning module, an information fusion and storage module, a convolutional neural network learning module, a model storage and screening module and a lesion detection module. The invention relates to the fields of deep learning, medical treatment and computer vision. By design of scientific optimization, a set of automatic intelligent detection system for coronary artery calcification, complete occlusion and thrombosis based on the convolutional neural network is created and achieved, aiming at the requirements of diagnosis on resultaccuracy and timeliness, the design structure is ingenious, a high-quality auxiliary diagnosis detection result can be output without any manual assistance, and convenience is brought to coronary artery patients and doctors.