Objective High-intensity interval training (HIIT) is a powerful way to enhance vascular function, and hypoxia may have an additional benefit on cardiorespiratory fitness. However, the effect of hypoxia and HIIT on hemodynamics is not clear. The purpose of the present study was to compare the effects of exercise mode and hypoxia on blood pressure, arterial stiffness, and heart rate variation (HRV) in sedentary young women. Methodology 31 female college students were randomly assigned into the groups of hypoxic high-intensity interval training (HHIT, simulated at an altitude of 2500 m), normoxic high-intensity interval training (NHIT, simulated at sea level), and continuous moderate-intensity training (MICT). They completed a 5-week exercise intervention with four days each week. HIIT and NHIT comprised 8s of maximal effort interspersed with 12s rest with a maximum of 80 repetitions in 20 min, while MICT performed 40 min at 60– 80% of peak oxygen consumption (VO2peak). Measures including brachial-ankle pulse wave velocity (baPWV), blood pressure (BP) and heart rate variability (HRV) were conducted at rest with a supine position before and after the exercise intervention. Results & Discussion After 5 weeks of exercise intervention, heart rate (p = .001) and the rate of pressure production (RPP) (p = .038) were significantly decreased, whereas VO2peak (p = .000) were significantly increased. There were no changes in blood pressure and baPWV after the 5-week training in all the three groups. In terms of the frequency domain of HRV analysis, low-frequency (LF) power decreased (p = .002), high-frequency (HF) power increased (p = .002), and the LF/HF ratio decreased (p = .013). With regard to time domain, the root mean square of the standard deviation of the R–R interval (RMSSD) was tended to increase (p = .070), while to non-linear components of HRV, SD1 of the sample entropy had a trend to be increased (p =.069). Conclusion The three modes of 5-weeks of exercise intervention are effective to improve cardiovascular fitness and heart rate variation in untrained young women. However, there are no mode differences on hemodynamics, despite HIIT being a time-efficient strategy.