Symptoms caused by SARS-CoV-2 infection usually last 5-7 days; however, people experiencing symptoms for more than 5-7 days were reported, in a phase called long-term COVID-19 or post-COVID-19. Due to the ease of disease transmission and viral susceptibility, mild or asymptomatic infections are prevalent among young individuals; however, few studies have focused on the differences in autonomic functions in LC patients versus those recovering from COVID-19. In this study, we collected heart rate variability indices from patients survived for more than two months after a negative secondary RT-PCR test. A total of 173 individuals were included through autonomic balance surveys and questionnaires, including 57 controls with no history of COVID-19 and 84 COVID-19 survivors in COVID-19 rehabilitation group and 32 LC patients in LC group. The results suggested that the reduction in the very low frequency domain was significant among groups, and that in those aged <25 years, more individuals showed abnormal autonomic neuroactivity in the LC group compared to the COVID-19 rehabilitation group. The different results suggest that autonomic dysfunction still exists in those who have experienced the long-covid phase, which could be caused by sympathetic activation and inhibition of vagal activity.