The microstructure of the bone-tendon interface (BTI) deserves in-depth investigation. In this study, we first aimed to extend the application of synchrotron radiation μCT to characterize the gradient structure of supraspinatus tendon (SST) enthesis, from both tissue morphology to cell distribution. Second, to acquire detailed morphological information of SST enthesis when after injury. Our results showed that in normal enthesis, the phenotype of chondrocyte in BTI was dependent on its distance to subchondral bone. After injury, the fibrocartilage cells were disrupted, as evidenced by reduced lacunae size. Our observation may partly explain the loss of BTI mechanical properties after injury, and we believe the application of synchrotron radiation microcomputed tomography will have promising potential for characterizing the morphology changes in enthesis and for evaluating the therapeutic effects of interventions in preclinical studies.