Mn–Fe Prussian blue analogs (PBAs) cathode materials suffer from poor cycling reversibility and capacity retention during phase transition from cubic to tetragonal phase, which is related to the large structural deformation of Mn−N6 octahedra caused by Jahn-Teller distortion. Herein, we explore a controllable strategy for creating unconventional cation Mn vacancies (VMn) on the surface of Mn–Fe PBAs by utilizing a strong chelating agent—ethylenediaminet etraacetic acid disodium. The VMn in Mn–Fe PBAs can restrain the movement of Mn−N bonds and thereby mitigate the Jahn-Teller distortion of Mn−N6 octahedra, leading to highly reversible phase transitions of Mn–Fe PBAs as well as an outstanding long-term cycling stability and capacity retention for both the half-cell (72.3% after 2,700 cycles at 0.5 A g−1) and full cell (75.5% after 550 cycles at 0.1 A g−1). This work opens up a universal avenue to explore the relationship between vacancies and electrochemical performances, even in other materials beyond PBAs.