Although it has been traditionally thought that decreasing SpO2 with ascent to high altitudes not only induces acute mountain sickness but also can decrease executive function, the relationship between decreased SpO2 levels and hypoxia-induced lowered executive function is still unclear. Here we aimed to clarify whether hypoxia-induced lowered executive function was associated with arterial oxygen desaturation, using 21 participants performing the color-word Stroop task under normoxic and three hypoxic conditions (FIO2 = 0.165, 0.135, 0.105; corresponding to altitudes of 2000, 3500, and 5000 m, respectively). Stroop interference significantly increased under severe hypoxic condition (FIO2 = 0.105) compared with the other conditions. Moreover, there was a negative correlation between Stroop interference and SpO2. In conclusion, acute exposure to severe hypoxic condition decreased executive function and this negative effect was associated with decreased SpO2. We initially implicated an arterial oxygen desaturation as a potential physiological factor resulting in hypoxia-induced lowered executive function.