Pulmonary vein isolation (PVI) has been widely used for the treatments of paroxysmal atrial fibrillation (PAF); however, AF recurrence remains a significant challenge. We evaluated relation between autonomic nervous activity and AF recurrence using heart rate variability (HRV) and deceleration and acceleration capacity (DC/AC) analyses. High-resolution Holter electrocardiogram was performed in 56 PAF patients pre- and 3 and 6 months post-PVI by cryoballoon. HRV and DC/AC analysis data were compared between the non-recurrence and recurrence groups. AF recurrence occurred in 10 cases. Total heart beats and maximum heart rate significantly decreased and minimum heart rate increased only in the non-recurrence group post-PVI. In HRV analysis, root mean square successive difference (RMSSD), low-frequency components (LF), high frequency components (HF) and LF/HF significantly decreased only in the non-recurrence group at both 3 and 6 months post-PVI; in contrast, significant decreases in RMSSD, LF and HF were observed in the recurrence group only at 6 months. In DC/AC analysis, DC significantly decreased in both groups post-PVI; in contrast, AC increased only in the non-recurrence group, resulting in significantly greater AC/DC ratio in the recurrence group at 3 months post-PVI. To prevent AF recurrence after PVI, it is important not only to reduce vagosympathetic overall activity but also to minimize imbalance between vagosympathetic reflex responses.