Abstract: Sodium superionic conductor-type Na₃MnTi(PO₄)₃ is a promising cathode for sodium-ion batteries. However, the anti-site defects due to the occupation of Na vacancies by Mn lead to voltage hysteresis and capacity loss. In this study, we present a method for efficient manipulating the e_g orbital of elemental Mn in the Na₃MnTi(PO₄)₃ to enhance the Mn–O covalent interaction. This modulation of the e_g orbital facilitates the electron filling in the Mn (3d–e_g) orbital and strengthens hybridization with the O (2p) orbital, which increases the formation energy of Mn defects and thereby effectively restrains anti-site defects in Na₃MnTi(PO₄)₃. The optimized Na_2.97Li_0.03MnTi(PO₄)₃ cathode delivers a capacity of 115.8 mAh g⁻¹ at 10 C (164.9 mAh g⁻¹ at 0.1 C), while retaining an outstanding capacity retention of 89.2% over 3000 cycles, along with stable cycling characteristics under temperatures ranging from −30 °C to 40 °C. The pouch-type full cell (50 × 35 × 5 mm³) using the Na_2.97Li_0.03MnTi(PO₄)₃ cathode and hard carbon anode further demonstrates its promising application. This study elucidates the anti-site defects suppression mechanism through molecular orbital analysis, offering new perspectives for developing high-performance sodium-ion cathode materials.