Abstract The Mn‐based phosphate Na 3+2x Mn 1+x Ti 1‐x (PO 4 ) 3 cathodes have attracted widespread attention for Na‐ion batteries owing to the abundant Mn resource and high Mn 2+ /Mn 3+ /Mn 4+ redox potential. However, they suffer from high voltage hysteresis and low reversible capacity at 2.5–4.2 V (60–80 mAh g−1) due to intrinsic anti‐site defects of Mn 2+ occupying Na2 vacancies. Although metal ion substitutions (e.g., V 3+ ) can reduce intrinsic anti‐site defects and improve reversible capacity (80–110 mAh g −1 ), the underlying mechanism remains not well‐understood, limiting further improvement of the reversible capacity. Here, five metal‐ion substitution cathodes: Na 3.4 Mn 1.15 Ti 0.75 M 0.1 (PO 4 ) 3 (M = Fe 3+ , Al 3+ , V 3+ , Cr 3+ , and Ga 3+ ) are systematically studied, among which only two metal ions (V 3+ and Cr 3+ ) can remarkably reduce intrinsic Mn 2+ /Na2 anti‐site defect and voltage hysteresis. The revealed mechanism is that V 3+ and Cr 3+ substitutions tend to form a MnO 5 polyhedron with the less Mn─O coordination numbers under the assumption of Mn 2+ occupying the Na2 vacancy, compared to the MnO 6 octahedron in other metal‐ion substitutions (Fe 3+ , Al 3+ , and Ga 3+ ). The formation of MnO 5 polyhedron indicates an energetically more unfavorable state for Mn 2+ /Na2 anti‐site defects. The designed Na 3.5 Mn 1.15 Ti 0.65 V 0.1 Cr 0.1 (PO 4 ) 3 cathode exhibits the lowest ratio of intrinsic anti‐site defect (0.28%) and achieves a high reversible capacity (120.7 mAh g −1 ) and high energy density (431.6 Wh kg −1 ), with superior cycling stability (93.2% retention after 2000 cycles at 5 C). This work offers valuable insights for designing high‐capacity and high‐energy Mn‐based Na‐ion cathodes.