Purpose: This descriptive study aimed to investigate heart rate variability (HRV) according to sex and to elucidate the influence of negative emotion such as levels of stress, anxiety and depression on HRV among Korean college students based on a neurovisceral integration model. Methods: A descriptive study design was used. Eighty-six healthy college students participated in the study. Resting HRV and standing HRV on orthostatic stimulation were measured for 5 minutes during 4-6 p.m. in the afternoon. Levels of stress, anxiety and depression were assessed using the Global assessment of recent stress, State-Trait Anxiety Inventory and Beck Depression Index, respectively. Results: Out of the 86 students, 47 (54.7%) were men and 39 (45.3%) were women. Root mean square of the differences between adjacent RR intervals (RMSSD) and normalized high frequency (nHF) on standing HRV were significantly lower in men than in women (p=.005, p=.019, respectively). Male gender (β=0.30, p=.013), higher level of stress (β=-0.36, p=.009) and lower level of depression (β=0.30, p=.044) exerted a significant influence on decreased nHF in the multiple regression analysis. Conclusion: We suggest that men are more vulnerable to having reduced vagal activity on HRV than women. Since male gender, higher level of stress and lower level of depression level influenced decreased vagal activity, strategies are needed to improve stress and depression rather than anxiety especially for men, which contribute to promoting HRV to prevent cardiac health diseases.