Heart sound analysis is significant for early diagnosis of congenital heart disease. A novel method of heart sound classification was proposed in this paper, in which the traditional mel frequency cepstral coefficient (MFCC) method was improved by using the Fisher discriminant half raised-sine function (F-HRSF) and an integrated decision network was used as classifier. It does not rely on segmentation of the cardiac cycle. Firstly, the heart sound signals were framed and windowed. Then, the features of heart sounds were extracted by using improved MFCC, in which the F-HRSF was used to weight sub-band components of MFCC according to the Fisher discriminant ratio of each sub-band component and the raised half sine function. Three classification networks, convolutional neural network (CNN), long and short-term memory network (LSTM), and gated recurrent unit (GRU) were combined as integrated decision network. Finally, the two-category classification results were obtained through the majority voting algorithm. An accuracy of 92.15%, sensitivity of 91.43%, specificity of 92.83%, corrected accuracy of 92.01%, and F score of 92.13% were achieved using the novel signal processing techniques. It shows that the algorithm has great potential in early diagnosis of congenital heart disease.