Nonlinear analyses of heart rate variability (HRV) can be used to quantify the unpredictability, fractal properties and complexity of heart rate. Fractality and its analysis provides valuable information about cardiovascular health. Multi-Scale Multi-Fractal Detrended Fluctuation Analysis (MSMFDFA) is a complexity-based algorithm that can be used to quantify the multi-fractal dynamics of the HRV time series through investigating characteristic exponents at different time scales. This method is applicable to short time series and it is robust to noise and nonstationarity. We have used MSMFDFA, which enables assessment of HRV in the frequency ranges encompassing the very-low frequency and ultra-low frequency bands, to jointly assess multi-scale and multi-fractal dynamics of HRV signals obtained from telemetric ECG recordings in wildtype mice at baseline and after autonomic nervous system (ANS) blockade, from electrograms recorded from isolated atrial preparations and from spontaneous action potential recordings in isolated sinoatrial node myocytes. Data demonstrate that the fractal profile of the intrinsic heart rate is significantly different from the baseline heart rate in vivo, and it is also altered after ANS blockade at specific scales and fractal order domains. For beating rate in isolated atrial preparations and intrinsic heart rate in vivo, the average fractal structure of the HRV increased and multi-fractality strength decreased. These data demonstrate that fractal properties of the HRV depend on both ANS activity and intrinsic sinoatrial node function and that assessing multi-fractality at different time scales is an effective approach for HRV assessment.