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.