In many previous reports, the engineering of nanostructures using electron beam irradiation (EBI) in a high vacuum has primarily been based on the knock-on atom displacement. Herein, we report a new phenomenon under EBI that can also be effectively used to engineer a nanostructure: local Coulomb explosion (LCE) of cantilevered multiwalled boron nitride nanotubes (BNNTs) resulted from their profound positive charging. The nanotubes are gradually shortened, while the tubular shells at free ends are torn into graphene-like pieces and then removed during LCE. The phenomenon is dependent not only on the characteristics of an incident electron beam, as in the case of a common knock-on process, but also on the cantilevered tube length. Only after the electron beam density and tube length exceed the threshold values can LCE take place, and the threshold value for one of the parameters decreases with increasing the value of the other one. A model based on the diffusion of electron-irradiation-induced holes along a BNNT is proposed to describe the positive charge accumulation and can well explain the observed LCE. LCE opens up an efficient and versatile way to engineer BNNTs and other dielectric nanostructures with a shorter time and a lower beam density than those required for the knock-on effect-based engineering.