Obstructive sleep apnea (OSA) with hypoxic consequence, a common and underdiagnosed medical condition, is considered as a high risk factor for onset Metabolic Syndrome (MetS) characterized by hyperglycemia, hypertension, and hypertriglyceridemia and so on. The pathophysiological mechanisms underlying OSA may involve sympathetic over-activation, inflammation, oxidative stress and insulin resistance (IR), with IR being the pivotal contributor. On the other hand, hypobaric hypoxia in high altitude exerts protective effects on organization metabolism such as IR improvement, hypertension prevention, down-regulation of sympathetic tone and inflammation factors and enhanced anti-oxidation. All these observations demonstrated that different hypoxic patterns from OSA and high altitude may lead to opposite biological effects. Here we reviewed the differential effects and relevant mechanisms of these two hypoxic patterns, which aimed to address the role of hypobaric hypoxia in MetS treatment.