Localized morphometric deformations of small airways and alveoli during respiration have many biomedical and physiological implications. We developed fast synchrotron radiation CT system to visualize the small airways and alveoli of an intact mouse lung without fixation and dehydration, and analyzed their localized morphometric deformations between functional residual capacity (FRC) and total lung capacity (TLC). In the diameter behavior, the averaged and range values were significantly larger for smaller airways (68.8%, range: 0.36–0.89) than larger airways (45.2%, range: 0.40–0.57). These results indicated that the airway did not deformed in same manner and that these morphological differences characterized the heterogeneous lung function.