Electromyographic (EMG) signals from muscles in the body torso are often contaminated by electrocardiography (ECG) interferences, which consequently compromise EMG intensity estimation. The ECG interference has become a barrier to proportional control of myoelectric prosthesis using a neural machine interface called targeted muscle reinnervation (TMR), which involves transferring the residual amputated nerves to nonfunctional muscles (typically pectoralis muscles for high level amputations). This study investigates a novel approach toward implementation of proportional myoelectric control by applying sample entropy (SampEn) analysis of surface EMG signals for robust intensity estimation in the presence of significant ECG interference. Surface EMG data from able-bodied and TMR amputee subjects with different degrees of ECG interference were used for performance evaluation. The results showed that the SampEn analysis had high correlation with surface EMG amplitude measurement but low sensitivity to different degrees of ECG interference. Taking this advantage, SampEn analysis of surface EMG signal can be used to facilitate implementation of proportional myoelectric control against ECG interference. This is particularly important for TMR prosthesis users.