Multi-scale entropy was introduced to analyze the blood oxygen sequence under hypoxic environment. Compared with mean analytical method, blood oxygen sequence analysis based on multi-scale entropy can reflect the dynamic adjustment mechanism of body hypoxia better. Multi-scale entropy, which is different from sample entropy that just estimates the difference between sequence length m and m＋1 on the smallest scale and ignores other scales, calculates sample entropy of time series on multiple scales and reflects the irregular degree of time series on scales. The result shows that blood oxygen sequence analysis based on multi-scale entropy can identify human hypoxia endurance. This method is a reliable analytical method for studying the mechanism of hypoxic regulation of human body. The result also shows that repeated hypoxic stimulation will produce acclimatization effects on the human body which shows memory of hypoxia environment.