As an indigenous species on the Tibetan Plateau, the yak is well adapted to the plateau hypoxic environment. The high-altitude hypoxia adaptation of the yak requires the adaptive reshaping of multiple tissues and organs, especially the lungs. To reveal the adaptive development of yak lungs under hypoxic stress at the tissue and molecular levels, we conducted histomorphological observations as well as transcriptomic and metabolomic studies of yak lungs at three ages (0.5, 2.5, and 4.5 years). The results showed that the lung tissue developed significantly with age. The mean alveolar area was higher (p < 0.01) in 4.5 and 2.5-year-old yaks than in 0.5-year-old yaks. The percentage of elastic fibers, micro-arterial wall thickness, and micro-arterial area showed an increasing trend (p < 0.01) from 0.5-year-old yaks to 2.5-year-old yaks and then to 4.5-year-old yaks. In addition, some critical differentially expressed genes related to angiogenesis (MYC, EPHA2, TNF), fiber formation (EREG), smooth muscle proliferation (HBEGF), erythropoiesis (SOCS3), and hypoxia response (ZFP36) were identified. Some metabolites associated with these genes were also found simultaneously. These findings provide a deeper understanding of the molecular strategies underlying this species’ extraordinary ability to survive normally in low-oxygen environments. In conclusion, the lungs of yaks undergo continuous adaptive development under hypoxic stress, and these findings are crucial for understanding the molecular mechanisms by which native species of the Tibetan Plateau survive in harsh environments.