The fetal electrocardiogram (ECG) could provide clinical information concerning physiological conditions of the fetus. In order to extract fetal ECG, we proposed the novel algorithm, the blind source separation with reference (BSSR), which successfully extracts a complete waveform of QRS complex and avoids uncertainty in the order of the extracted signals. In the BSSR, the reference signal is supposed to be generated from the ultrasonic Doppler signal. Thus generated reference is expected to suffer from uncertainties in waveform and occurrence timing. Based on simulations, the BSSR is shown to have robustness against the uncertainties of reference signals. In addition, it is shown how the robustness depends on the order of power of correlation function between the reference and extracted signals, which composes a performance function of the BSSR.