The study presents a mathematical model of non-linear dynamics of the heart rate variability (HRV). The model is based on quantitative characteristics of pulse conduction in the heart conducting system: the delays of sinoatrial (SA) and atrioventricular (AV) pulse conduction and refractors periods of the SA and AV nodes. The model predicts heart rate disturbances in fast electric activity of the atria, increase in the delay of the AV conduction, the critical value of atrial period where transition to non-linear dynamics of the heart rate variability starts. The correlation between indexes of HRV and period of stimulation of atria for 1-contour cardiac control model has been demonstrated.