Beryllium was chosen as a plasma-facing material (PFM) for the first wall in an international thermonuclear experimental reactor (ITER). In this study, the deuterium and helium retention behavior in Be and the associated microstructure evolution were investigated using thermal desorption spectroscopy (TDS) and transmission electron microscopy (TEM). Since the disappearance of bubbles was observed at desorption peak temperatures of about 773 K for deuterium and 973 K for helium, these desorption peaks could be attributed to the release from each bubble. The existence of deuterium or helium within each bubble was also clearly confirmed using electron energy-loss spectroscopy (EELS) combined with scanning transmission electron microscopy (STEM). There was a clear difference between the disappearance process of the deuterium and helium bubbles. While the deuterium bubble gradually shrunk and disappeared, the helium bubble instantly vanishes. The results showed that the stability of helium bubbles was higher than that of deuterium bubbles.