Membrane capacitive deionization (MCDI) technology is a promising water quality desalination technology. It is reasonably necessary to find suitable electrode materials with unique properties for high desalination performance. Herein, fish scales (FSs) are selected as precursors for obtaining carbon materials with a hierarchical porous structure with the contributions from hydroxyapatites (HAs) templates, which are naturally contained in the FSs. The characterizations of the derived carbon show that it possesses an ultra-high specific surface area of 3,761.71 m2 g−1, a lot of micro/mesopores, natural heteroatomic doping sites and excellent wettability. As a result, it shows an excellent desalination capacity of 29.14 mg g−1 and good electrode regeneration performance, proving that the fish scales-derived carbon is promising for MCDI application.