Congenital Heart Disease (CHD) is the most common neonatal anomaly, highlighting the urgent need for early detection to improve outcomes. Yet, fetal ECG (fECG) signals in abdominal ECG (aECG) are often masked by maternal ECG and noise, challenging conventional methods under low signal-to-noise ratio (SNR) conditions. We propose FetalHealthNet (FHNet), a deep learning framework that integrates Graph Neural Networks with a multi-scale enhanced transformer to dynamically model spatiotemporal inter-lead correlations and extract clean fECG signals. On benchmark aECG datasets, FHNet consistently outperforms long short-term memory (LSTM) models, standard transformers, and state-of-the-art models, achieving R2>0.99 and RMSE = 0.015 even under severe noise. Interpretability analyses highlight physiologically meaningful temporal and lead contributions, supporting model transparency and clinical trust. FHNet illustrates the potential of AI-driven modeling to advance fetal monitoring and enable early CHD screening, underscoring the transformative impact of next-generation biomedical signal processing.