Nanoinstability and nanoprocessing of a SiOx amorphous nanowire at room temperature as induced by in situ electron beam irradiation in transmission electron microscopy are systematically investigated. It is demonstrated that in contrast to the crystalline nanowires where only the beam-induced ablation of atoms was observed, the amorphous nanowire herein can give rise to an arresting beam-induced surface-extruded plastic flow of massive atoms and surface migration of atoms in addition to the beam-induced ablation of atoms. Via the plastic flow and ablation, a new S-type deformed wire and the thinnest amorphous nanowire are elaborately created locally at nanoscale precision with a highly controllable manner depending on the beam current density, beam spot size, and beam position. The existing knock-on mechanism and simulation seem inadequate to explain these processes. However, it is indicated that a much higher nanocurved surface energy of nanowires and an enhanced beam-induced soft mode and instability of atomic vibration control the processes.