Muscle metaboreflex activation during hypercapnia leads to enhanced pressive effects that are poorly understood while autonomic responses including baroreflex function are not documented. Thus, we assessed heart rate variability (HRV) that is partly due to autonomic influences on sinus node with linear tools (spectral analysis of instantaneous heart period), baroreflex set point and sensitivity with the heart period-arterial pressure transfer function and sequences methods, and system coupling through the complexity of RR interval dynamics with nonlinear tools (Poincare plots and approximate entropy (ApEn)). We studied ten healthy young men at rest and then during muscle metaboreflex activation (MMA, postexercise muscle ischemia) and hypercapnia (HCA, PetCO2 = + 10 mmHg from baseline) separately and combined (MMA + HCA). The strongest pressive responses were observed during MMA + HCA, while baroreflex sensitivity was similarly lowered in the three experimental conditions. HRV was significantly different in MMA + HCA compared to MMA and HCA separately, with the lowest total power spectrum (p < 0.05), including very low frequency (p < 0.05), low frequency (p < 0.05), and high frequency (tendency) power spectra decreases, and the lowest Poincare plot short-term variability index (SD1): SD1 = 36.2 ms (MMA + HCA) vs. SD1 = 43.1 ms (MMA, p < 0.05) and SD1 = 46.1 ms (HCA, p < 0.05). Moreover, RR interval dynamic complexity was significantly increased only in the MMA + HCA condition (ApEn increased from 1.04 +/- 0.04, 1.07 +/- 0.02, and 1.05 +/- 0.03 to 1.10 +/- 0.03, 1.13 +/- 0.04, and 1.17 +/- 0.03 in MMA, HCA, and MMA + HCA conditions, respectively; p < 0.01). These results suggest that in healthy young men, muscle metaboreflex activation during hypercapnia leads to interactions that reduce parasympathetic influence on the sinus node activity but complexify its dynamics.