Blood oxygen saturation (SpO2) is a key indicator of oxygen availability in the body. It is known that a low SpO2 at high altitude is associated with morbidity and mortality risks due to physiological hypoxemia. Previously, it was proposed that the lowlander immigrants living at high altitude should have a lower SpO2 level compared to the highlander natives, but this proposal has not been rigorously tested due to the lack of data from the lowlander immigrants living at high altitude. In this study, we compared arterial oxygen saturation of 5929 Tibetan natives and 1034 Han Chinese immigrants living at altitudes ranging from 1120 m to 5020 m. Unexpectedly, the Han immigrants had a higher SpO2 than the Tibetan natives at the same high altitudes. At the same time, there is a higher prevalence of chronic mountain sickness in Han than in Tibetans at the same altitude. This result suggests that the relatively higher SpO2 level of the acclimatized Han is associated with a physiological cost, and the SpO2 level of Tibetans tends to be sub-optimal. Consequently, SpO2 alone is not a robust indicator of physiological performance at high altitude. The online version contains supplementary material available at 10.1007/s43657-023-00117-x.