Purpose <p>Comparative knowledge of cardiac autonomic dysfunction between apnea and hypopnea events is limited. This study aimed to investigate the differences in cardiac autonomic dysfunction between apnea-predominant and hypopnea-predominant in patients with obstructive sleep apnea (OSA).</p> Methods <p>This was a single-center retrospective study conducted at Kangwon National University Hospital. Patients were selected based on standard polysomnographic diagnostic criteria for OSA. Patients were categorized into apnea- or hypopnea-predominant groups according to the proportion of apneas within apnea-hypopnea index (AHI) and matched for age, sex, and AHI. Heart rate variability (HRV) metrics were calculated from nocturnal electrocardiogram. SPSS version 20.0 was used for statistical analyses.</p> Results <p>Polysomnographic parameters (AHI, oxygen desaturation index, arousal, and oxygen saturation) of 473 patients correlated with HF, LF/HF, and low frequency normalized unit (LFnu). In the matched cohort, no differences were found between the two groups in basic characteristics, except the hypopnea-predominant group had a higher body mass index (28.9 ± 4.6 vs. 27.1 ± 3.6, respectively, <i>p</i> = 0.003, Cohen’s d = 0.44). Frequency domain analyses showed comparable results: TP (<i>p</i> = 0.450), VLF (<i>p</i> = 0.862), LF (<i>p</i> = 0.514), and HF (<i>p</i> = 0.251). Additionally, for apnea-predominant and hypopnea-predominant groups, LF/HF (3.1 ± 1.9 vs. 3.1 ± 2.1, respectively; <i>p</i> = 0.968, Cohen’s d = 0.00) and LFnu (70.7 ± 11.8 vs. 69.3 ± 13.7, respectively; <i>p</i> = 0.480, Cohen’s d = 0.11) were comparable.</p> Conclusion <p>No significant differences were found in HRV ​​between the apnea-predominant and hypopnea-predominant groups after matching for age, sex, and AHI. Therefore, the cardiac autonomic dysfunctions associated with apnea and hypopnea events should be considered equivalent in patients with OSA.</p>