Heart failure (HF) is a complicated clinical illness caused by a variety of primary and secondary causes, as well as increased infection pathways, that are associated with higher risk, illness, and costs. The overall incidence of congenital heart disease is approximately high and is the leading cause of death in infants and children. In this study, we present a novel computational model based on ECNN-LSTM for detecting congenital heart disease in real time and assessing its developing course objectively. The proposed model is a multiresolution singular value decomposition for congenital heart disease prediction in infants and children. Firstly, in the whole-life vibration time-domain signal of newborns and toddlers, the multiresolution singular value decomposition approach is employed to create approximation and detailed signals with different resolutions. Secondly, the health phases are split into the smooth running stage of newborns and toddlers, as well as the standard deviation of the earliest moments. Thirdly, the two-layer one-dimensional convolutional neural network structure divides the quick degradation stage, which can offer degradation information. Finally, the prediction of congenital heart disease is finished on LSTM utilizing the MSE loss function to unify the assessment scale. Validation with lifespan data demonstrates the feasibility and effectiveness of the proposed model. Moreover, the existing models have the insufficient ability for life span feature characterization in congenital heart disease prediction in infants and children.