This study investigates the effect of electron-beam heating in transmission electron microscopy (TEM) on the structure of antimony (Sb) thin films. TEM of Sb irradiated with 300 keV electrons reveals a significant deviation (2–3°) from the theoretical interplanar angle between certain planes within the irradiated region. We relate this anomaly to electron-beam heating under electron-beam irradiation. Our FEA simulations reveal localized heating within the irradiated region caused by Auger electron excitation. These simulations predict temperatures as high as 949 K, accompanied by ultrafast heating and quenching rates. This extreme thermal cycling likely induces significant thermal stress in localized regions, possibly exceeding their elastic limits. This stress is likely related to the observed structural anomalies. This work highlights the importance of considering beam heating, particularly when interpreting TEM data from nanoscale materials with reduced thermal conductivity due to surface scattering effects.