Abstract Constructing heterostructure for synergistic effect plays an indispensable role in enhancing the energy density and cycling stability of layered oxide for sodium‐ion batteries. However, the mechanisms of heterostructure formation and synergistic effects remain inadequately understood. In this study, the strategy of controlling oxygen vacancies is carried out based on Na 2 Mn 3 O 7 cathode material. The formation of oxygen vacancy can change the coordination environment of Mn and Na + occupancy between MnO 2 layers, which is a significant driving force for structure transitions. Furthermore, the ratio of lattice oxygen to vacancy oxygen (L O /V O ) demonstrates a distinct nonlinear relationship with the structural proportion in heterostructure materials, which can be used as a critical descriptor for evaluating the structural proportion. The obtained heterostructure with Na 2 Mn 3 O 7 (, 55 wt.%), P2‐Na 0.67 MnO 2 (P6 3 /mmc, 40 wt.%) and O′3‐NaMnO 2 (C/2 m, 5 wt.%) retains anionic redox characteristics, exhibits a high specific capacity of 245 mAh g −1 with an energy density of 596 Wh kg −1 . The formation of heterogeneous interfaces provides numerous Na + insertion/extraction sites and the presence of a minor amount of O′3‐NaMnO 2 effectively mitigates the Jahn‐Teller effect at low voltages, enhancing structural stability. This work offers new insights into the rational design and application of heterostructure layered oxide cathodes.