Periodic deep slow breathing at specific frequencies can induce baroreflex resonance through the heart rate-baroreflex pathway, referred to as resonance breathing. In recent years, the application of heart rate variability (HRV) in assessing autonomic function has been questioned, whereas the novel, noninvasive measurement of skin sympathetic nerve activity (SKNA) may fill certain gaps. This study aimed to explore the effects of resonance breathing on SKNA and HRV from the perspective of autonomic indices, evaluating its acute physiological impacts on a healthy population. A randomized crossover design was employed, recruiting 27 healthy university students (14 males, 13 females) as participants. The experimental protocol consisted of a 10-minute resting period, a 15-minute resonance breathing intervention, and a 5-minute post-intervention rest phase, during which SKNA and HRV were continuously monitored and evaluated. The results showed a significant increase in sympathetic nerve activity during the resonance breathing intervention phase, followed by notable reductions in both average sympathetic activity and burst-derived parameters post-intervention. In addition, HRV indicators, particularly RMSSD and RR interval, were markedly elevated after the intervention. These findings suggest that a single session of resonance breathing exerts positive effects on autonomic function, providing a basis for considering the combined use of resonance breathing and SKNA techniques over longer durations in pathological populations for autonomic regulation.