Bone-tendon junction (BTJ) injury is difficult to cure due to its special anatomical structure. Most methods applied for BTJ injury treatment cannot lead to the perfect restoration of the fibrocartilage zone and perfect vascular regeneration, which are two important facets of BTJ reconstruction. Based on current research, hypoxia, which has been discovered to induce chondrogenesis and angiogenesis in vivo, plays an essential role in the tissue repair process. Consequently, it is reasonable to confirm that a hypoxic environment is the prerequisite condition to obtain physiological healing of BTJ injury. In this paper, the potential relationship between hypoxia and BTJ healing is discussed. Moreover, an operation model and possible drug application to obtain hypoxic conditions are delineated.