Despite the widespread use of charge-trap flash (CTF) memory, the atomistic mechanism behind the exceptionally stable charge storage at the localized trap sites is still controversial. Herein, by combining first-principles calculations and orbital interaction analysis, a charge-dependent switchable chemical-bond reorganization is elucidated as the underpinning chemistry in the working mechanism of CTF. Especially, positively charged fourfold-coordinated nitrogen (dubbed N⁺ center), unappreciated until now, is the decisive component of the entire process; once an electron occupies this site, the N⁺ center disappears by breaking one N─Si bond, simultaneously forming a new Si─Si bond with a nearby Si atom which, in turn, creates fivefold coordinated Si. As a result, the electron is stored in a multi-center orbital belonging to multiple atoms including the newly formed Si─Si bond. It is also observed that hole trapping accompanies the creation of an N⁺ center by forming a new N─Si bond, which represents the reverse process. To further support and validate this model by means of core-level calculations, it is also shown that an N⁺ center's 1s core level is 1.0–2.5 eV deeper in energy than those of the threefold coordinated N atoms, in harmony with experimental X-ray photoelectron spectroscopy data.