Fetal heart monitoring, as a crucial part of fetal monitoring, can accurately reflect the fetus’s health status in a timely manner. To address the issues of high computational cost, inability to observe fetal heart morphology, and insufficient accuracy associated with the traditional method of calculating the fetal heart rate using a four-channel maternal electrocardiogram (ECG), a method for extracting fetal QRS complexes from a single-channel non-invasive fetal ECG based on a multi-feature fusion neural network is proposed. Firstly, a signal entropy data quality detection algorithm based on the blind source separation method is designed to select maternal ECG signals that meet the quality requirements from all channel ECG data, followed by data preprocessing operations such as denoising and normalization on the signals. After being segmented by the sliding window method, the maternal ECG signals are calculated as data in four modes: time domain, frequency domain, time–frequency domain, and data eigenvalues. Finally, the deep neural network using three multi-feature fusion strategies—feature-level fusion, decision-level fusion, and model-level fusion—achieves the effect of quickly identifying fetal QRS complexes. Among the proposed networks, the one with the best performance has an accuracy of 95.85% and sensitivity of 97%.