Purpose: This study aimed to present a preliminary case analysis of the impact of regular and irregular exercise on autonomic regulation and cardiorespiratory performance in young women by comprehensively investigating the nocturnal heart rate variability (HRV) parameters. Methods: Two young female participants were monitored using noncontact ballistocardiography technology to assess their nocturnal HRV daily for 32 weeks. Participant 1 was a 28-year-old woman who engaged in regular running (approximately three times a week, 5km each time), and participant 2 was a 24-year-old woman who participated in irregular running (typically ≤3 times a week, 5km each time). Additionally, cardiorespiratory fitness was evaluated through maximal oxygen uptake (VO2max), with running data and VO2max measurements recorded using a wrist bracelet device. Results: During the experiment, the VO2max value of participant 1 increased by 11.46%, whereas that of participant 2 increased by 3.42%. A correlation was observed between VO2max and HRV, particularly in the high-frequency (HF) component. The correlation coefficient between ln HF and VO2max of participant 1 was 0.64, whereas that of participant 2 was 0.28. Additionally, participant 1 exhibited lower HRV complexity than participant 2, with fuzzy entropy values for ln HF of 0.12 and 0.35, respectively. Conclusions: Long-term assessment revealed a correlation between VO2max and nocturnal HRV in young female exercisers, particularly for the HF index. However, these findings may not apply to other populations, such as men or older individuals.