Sleep apnea hypopnea syndrome (SAHS) is an independent risk factor for cardiovascular diseases. However, the pathophysiology between them is not yet clear. This paper seeks to understand how respiratory events impact the cardiovascular system by heart rate variability. We compared the differences between successional pathological respiratory events (PR) and pure normal respiration (NR) during sleep. The transitions between normal and pathological respiration (TR) were also analyzed. Thirteen patients who suffered moderate or severe SAHS were enrolled in this study. The results demonstrate that the beat-to-beat interval (RR interval) mean value and sample entropy are significantly lower during PR than during NR. RR interval standard deviation, the power of very low frequency (VLF) and low frequency (LF), total power, and the low frequency/high frequency (LF/HF) ratio were significantly larger during PR than during NR. However, the high frequency (HF) power was not significantly different between normal and pathological respiration. Additionally, the trends during TR also supported these significant differences. The results indicate that during pathological respiration, as the heart rate and its volatility increase, the complexity of its rhythm decreases. We conclude that the energy of the autonomic nervous system rapidly increases during pathological respiration, especially at the beginning. The HF power does not significantly change to modulate the heart rhythm, but the activity of the sympathetic nervous system will significantly increase, resulting in the imbalance of the LF/HF ratio. In addition to these findings, this paper discusses the influence of arousal on these indices during TR.