Analyzing heart sound signals presents a novel approach for early diagnosis of pediatric congenital heart disease. The existing segmentation algorithms have limitations in accurately distinguishing the first (S1) and second (S2) heart sounds, limiting the diagnostic utility of cardiac cycle data for pediatric pathology assessment. This study proposes a time bidirectional long short-term memory network (TBLSTM) based on multi-scale analysis to segment pediatric heart sound signals according to different cardiac cycles. Mel frequency cepstral coefficients and dynamic characteristics of the heart sound fragments were extracted and input into random forest for multi-classification of congenital heart disease. The segmentation model achieved an overall F1 score of 94.15% on the verification set, with specific F1 scores of 90.25% for S1 and 86.04% for S2. In a situation where the number of cardiac cycles in the heart sound fragments was set to six, the results for multi-classification achieved stabilization. The performance metrics for this configuration were as follows: accuracy of 94.43%, sensitivity of 95.58%, and an F1 score of 94.51%. Furthermore, the segmentation model demonstrates robustness in accurately segmenting pediatric heart sound signals across different heart rates and in the presence of noise. Notably, the number of cardiac cycles in heart sound fragments directly impacts the multi-classification of these heart sound signals.