Hypoxia is a representative stress environment, under which cell energy and oxidative metabolism change a lot. Among the product of metabolism, reactive oxygen species (ROS) which generate from mitochondria under hypoxia seriously threaten cell survive. Mitophagy was recently found as an adaptive metabolic response to hypoxia. Cell induces mitophagy by the pathway mediated by BNIP3/BNIP3L and Beclin-1 that are activated by up-regulation of HIF-1 under hypoxia, then reduces the production of ROS, and ultimately promotes cell survival. This process leads to the adaptation of organism to hypoxia. In this paper, we will overview the role and the mechanism of mitophagy in adaptation to hypoxia.