This study intended to study the effects of altitude in the high-rise building on the automatic nervous modulation in healthy subjects. Heart rate variability (HRV) analysis was performed to assess the automatic nervous modulation of the subjects at three different altitudes in the air-conditioned high-rise building, i.e., the first basement (4 m beneath sea level), the 31st floor (133 m above sea level), and the 46 th floor (200 m above sea level). We found that the heart rate was significantly decreased, whereas the standard deviation of RR intervals (SD(RR)), total power and high frequency power were significantly increased when the subject was elevated to a higher altitude. The normalized low frequency power and low-/high-frequency power ratio on the 31st and 46 th floors were significantly different between genders; however, no such difference was found on the first basement. The age correlated significantly and positively with the percentage change in the SD(RR) and coefficient of variation of RR intervals when the subjects were elevated from the first basement to the 46 th floor. In conclusion, higher altitude in an air-conditioned high-rise building can lead to an increase in HRV/vagal modulation. The stay at a higher altitude in a high-rise building may lead to increased overall HRV and vagal modulation of a subject, especially for the elder people and the people who had a small HRV at ground level.