Objective To explore the effect of objective sleep quality on cardiac autonomic function in patients with obstructive sleep apnea (OSA). Methods A total of 3442 subjects suspected of OSA were enrolled. Sleep parameters were obtained via polysomnography, cardiac autonomic function was evaluated using heart rate variability (HRV) indicators, and multiple linear regression and mediation analysis were employed to clarify the associations and action pathways. Results With the increase in OSA severity, the proportions of sleep stages 1 and 2 and the microarousal index (MAI) increased, while the proportions of slow-wave sleep and rapid eye movement (REM) sleep decreased. The mean heart rate (MEANHR) and LF/HF ratio elevated, but the change trend of the standard deviation of normal-to-normal intervals (SDNN) was not entirely consistent with OSA severity. Multiple regression analysis showed that the proportion of REM sleep was independently negatively correlated with MEANHR, the proportion of sleep stage 1 was independently positively correlated with LF/HF, MAI was independently positively correlated with SDNN, and the apnea-hypopnea index (AHI) was significantly associated with all the aforementioned HRV indicators. Mediation analysis confirmed that objective sleep quality was an important mediator in the association between AHI and HRV indicators: MAI had the strongest mediating effect (accounting for 74.85% of the total effect), followed by the proportion of REM sleep ( 2.75% ) and sleep stage 1 ( 7.08% ) . Conclusion The objective sleep quality of OSA patients deteriorates with the aggravation of OSA severity. Elevated MAI is the most significant mediator of cardiac autonomic function impairment, and the treatment of OSA needs to simultaneously improve hypoxia and sleep quality.