A variety of heart rate variability (HRV) indices have been reported to estimate sleep stages, but the associations are modest and lacking solid physiological basis. Non-REM (NREM) sleep is associated with increased regularity of respiratory frequency, which results in the concentration of high frequency (HF) HRV power into a narrow frequency range. Using this physiological feature, we developed a new HRV sleep index named Hsi to quantify the degree of HF power concentration. We analyzed 11,636 consecutive 5-min segments of electrocardiographic (ECG) signal of polysomnographic data in 141 subjects and calculated Hsi and conventional HRV indices for each segment. Hsi was greater during NREM (mean [SD], 75.1 [8.3]%) than wake (61.0 [10.3]%) and REM (62.0 [8.4]%) stages. Receiver-operating characteristic curve analysis revealed that Hsi discriminated NREM from wake and REM segments with an area under the curve of 0.86, which was greater than those of heart rate (0.642), peak HF power (0.75), low-to-high frequency ratio (0.77), and scaling exponent α (0.77). With a cutoff >70%, Hsi detected NREM segments with 77% sensitivity, 80% specificity, and a Cohen’s kappa coefficient of 0.57. Hsi may provide an accurate NREM sleep maker for ECG and pulse wave signals obtained from wearable sensors.