This study explored the performance of multiscale entropy (MSE) for the assessment of mobile ECG signal quality, aiming to provide a reasonable application guideline. Firstly, the MSE for the typical noises, that is, high frequency (HF) noise, low frequency (LF) noise, and power-line (PL) noise, was analyzed. The sensitivity of MSE to the signal to noise ratio (SNR) of the synthetic artificial ECG plus different noises was further investigated. The results showed that the MSE values could reflect content level of various noises contained in the ECG signals. For the synthetic ECG plus LF noise, the MSE was sensitive to SNR within higher range of scale factor. However, for the synthetic ECG plus HF noise, the MSE was sensitive to SNR within lower range of scale factor. Thus, a recommended scale factor range within 5 to 10 was given. Finally, the results were verified on the real ECG signals, which were derived from MIT-BIH Arrhythmia Database and Noise Stress Test Database. In all, MSE could effectively assess the noise level on the real ECG signals, and this study provided a valuable reference for applying MSE method to the practical signal quality assessment of mobile ECG.