In this study, we explore the effect of electron-beam irradiation on the mechanical behavior of amorphous silica nanostructures. It has been reported that amorphous silica exhibits ductile deformation behavior under the electron-beam irradiation during the in-situ compression testing. However, the dependency of electron-beam conditions such as acceleration voltages and beam currents has not been thoroughly investigated. Hence, we performed in-situ mechanical testing for amorphous silica nanostructures at various electron-beam conditions. By systematically changing acceleration voltages and electron-beam currents, we found the thresh-hold electron-beam condition to induce plastic deformation of amorphous silica. Furthermore, our simulation study suggests that the electron-beam effect has clear correlation with the interaction volume of the electron-beam with the sample.