Cardiac auscultation is a noninvasive, convenient, and low-cost diagnostic method for heart valvular disease, and it can diagnose the abnormality of the heart valve at an early stage. However, the accuracy of auscultation relies on the professionalism of cardiologists. Doctors in remote areas may lack the experience to diagnose correctly. Therefore, it is necessary to design a system to assist with the diagnosis. This study proposed a computer-aided heart valve disease diagnosis system, including a heart sound acquisition module, a trained model for diagnosis, and software, which can diagnose four kinds of heart valve diseases. In this study, a training dataset containing five categories of heart sounds was collected, including normal, mitral stenosis, mitral regurgitation, and aortic stenosis heart sound. A convolutional neural network GoogLeNet and weighted KNN are used to train the models separately. For the model trained by the convolutional neural network, time series heart sound signals are converted into time-frequency scalograms based on continuous wavelet transform to adapt to the architecture of GoogLeNet. For the model trained by weighted KNN, features from the time domain and time-frequency domain are extracted manually. Then feature selection based on the chi-square test is performed to get a better group of features. Moreover, we designed software that lets doctors upload heart sounds, visualize the heart sound waveform, and use the model to get the diagnosis. Model assessments using accuracy, sensitivity, specificity, and F1 score indicators are done on two trained models. The results showed that the model trained by modified GoogLeNet outperformed others, with an overall accuracy of 97.5%. The average accuracy, sensitivity, specificity, and F1 score for diagnosing four kinds of heart valve diseases are 98.75%, 96.88%, 99.22%, and 97.99%, respectively. The computer-aided diagnosis system, with a heart sound acquisition module, a diagnostic model, and software, can visualize the heart sound waveform and show the reference diagnostic results. This can assist in the diagnosis of heart valve diseases, especially in remote areas, which lack skilled doctors.