Developing high-performance defect-rich carbon materials with abundant accessible active sites is exceedingly vital for electrochemical water desalination, but this still remains a significant challenge. Herein, a reverse-defect-engineering strategy is reported to synthesize high edge-nitrogen-doped nanotube-like carbon through the annealing process of protonated g-C3N4 under H2 atmosphere. The hydrogen bonds interaction between the proton and nitrogen atoms performs a crucial role in regulating nitrogen configurations. The nitrogen-doped carbon obtained from HCl pretreatment (HCl-NC) reduces the proportion of graphitic N and exhibits a high ratio of pyrrolic N to pyridinic N. Thus, the resulting synergetic structure of high edge-type N and small graphitic carbon nanodomains ensures more accessible active sites and fast charge-transfer kinetics simultaneously, contributing to high desalination capacity (100.3 mg g−1 at 1.2 V), fast time-average specific adsorption rate (1.7 mg g−1 min−1), low energy consumption (82.9 kJ molNaCl−1), and superior cyclic stability (no signs of performance decay after long-term cycling). The Na+-intercalation mechanism and structure-response relationship of HCl-NC are revealed by the electrochemical quartz crystal microbalance with dissipation monitoring and density functional theory calculations, respectively. This study provides a novel idea to modulate the nanotube-like, nitrogen-containing configurations for engineering carbon nanomaterials for advanced electrochemical applications.