The complex fluctuation of heart rate variability reflects the autonomous regulation function of the heart. In this paper, a novel method of measuring the heart rate variability is proposed. Firstly, the heart rate variability signal is decomposed by the improved complete ensemble empirical mode decomposition with adaptive noise method, and the multiple intrinsic mode functions are obtained, and the bubble entropy of each intrinsic mode function is calculated to obtain an entropy value vector. Then, the vector is mapped to a network based on a limited penetrable horizontal visibility graph method. By calculating various characteristic parameters of the network, the coupling relationship between the nonlinear features of heart rate variability in different time-frequency scale states are studied. The characteristic parameters include mean value of aggregation coefficient (MC), the characteristic path length (CL), the topological entropy of network (TE), the network level weighted bubble value (WB), and the pseudo mean value of node weight (PW). Firstly, the heart rate variabilities of 29 patients with congestive heart failure and 29 normal sinus heart rhythm subjects are analyzed by time domain, frequency domain and ICBN analysis method, the T test is used for statistical analysis, and Fisher discriminant method is used for classification. The results show that the time domain triangular index HRVTI, frequency domain index LF/HF, WB, PW and CL in ICBN have statistical differences. The accuracy rate of recognition model based on WB, CL, frequency domain index LF/HF and Fisher discriminant method is 89.66%. Secondly, the heart rate variabilities of 43 patients with atrial fibrillation arrhythmia and another 43 normal sinus heart rhythm subjects are analyzed by the same methods, including the time domain analyzed method, frequency domain analyzed method, and ICBN analyzed method. Then, the T test is also used for statistical analysis, and Fisher discriminant method is used for classification. The results show that using the time domain index pNN5 and RMSSD, frequency index LF/HF, ICBN index WB and PW as the feature vectors, and the Fisher discriminant mode as the classifier, the accuracy rate of recognition for atrial fibrillation arrhythmia is 91.86%. From these results it is concluded that the ICBN method provides a new idea for the heart rate variability measurement.