An internal shrinkage of nanocavity in silicon was in situ observed under irradiation of energetic electron on electron transmission microscopy. Because there is no addition of any external materials to cavity site, a predicted nanosize effect on the shrinkage was observed. At the same time, because there is no ion cascade effect as encountered in the previous ion irradiation-induced nanocavity shrinkage experiment, the electron irradiation-induced instability of nanocavity also provides a further more convincing evidence to demonstrate the predicted irradiation-induced athermal activation effect.