Acute mountain sickness, one of the most common altitude diseases, causes lung and brain injury. The present study aimed to investigate the anti‑hypoxic effect of purified polysaccharides extracted from Cordyceps militaris. The aqueous extract of Cordyceps militaris was purified progressively through a DEAE‑52 cellulose anion exchange column and a Sepharose G‑100 column. The fraction CMN1, with a molecular weight of 37842 Da, was the main fraction obtained and its chemical composition and structural characteristics were determined. CMN1 was found to have a monosaccharide composition of L‑rhamnose, L‑arabinose, D‑mannose, D‑galactose. The backbone of CMN1 comprised (1→2) and (1→3) linkages, with branched (1→6) and (1→4) linkages. The anti‑hypoxic effects of CMN1 were determined using a sodium nitrite toxicosis test, acute cerebral ischemic/hypoxic test and normobarie hypoxia test. CMN1 (0.5 g/kg) possessed a similar anti‑hypoxic effect to rhodiola oral liquid. Overall, the Cordyceps militaris polysaccharide, CMN1, was identified as an effective agent against hypoxia.