Obesity is a risk factor of cardiovascular disease-related mortality and may be associated with changes in the autonomic nerve activity. Nurses working shifts and caring for patients are under great mental and physical pressure, and research has proven that these can negatively affect the body. The objective of this study was to examine the influence of obesity in nurses on their heart rate variability (HRV) and determine whether age or shift type moderates this influence. A questionnaire survey and HRV measurements were conducted on nurses at a hospital in Taiwan during a routine employee health checkup. HRV analysis was conducted using a noninvasive HRV monitor for five minutes. A total of 242 nurses with a mean age of 28.98±6.56 years were enrolled in this study. An overly large waist circumference (WC) had a negative impact on high frequency (HF), low frequency (LF), and standard deviation of normal-to-normal interval (SDNN), while an overly high body mass index (BMI) had a negative impact on very low frequency (VLF) and SDNN. The interaction term “overly large WC × age” had a negative impact on HF (β=−0.21, p=0.010) and LF (β=−0.18, p=0.030), whereas the interaction term “overly high BMI×age” had a negative impact on HF (β=−0.27, p=0.001), LF (β=−0.19, p=0.023), and VLF (β=−0.17, p=0.045). The interaction terms “overly large WC × shift type” and “overly high BMI × shift type” did not influence any HRV parameters. As age increased, so did the degree to which the HF and LF of nurses with an overly large WC were lower than normal, and so did the degree to which the HF, LF, and VLF of nurses with an overly high BMI were lower than normal.