NaNi1/3Fe1/3Mn1/3O2 is recognized for its relatively high theoretical specific capacity and operating voltage, rendering it a sodium-ion cathode material with significant commercial potential. A higher cutoff voltage typically enables more sodium ion deintercalation, thereby achieving higher capacity. However, this increased deintercalation can introduce challenges such as structural instability and side reactions with the electrolyte, leading to electrochemical performance degradation. This study focuses on the migration process of transition metal ions under conditions of high charging cutoff voltage and high sodium removal. At a voltage of 4.3 V, the migration of Ni ions facilitates more charge compensation but is accompanied by irreversible Ni migration, inducing an irreversible phase transition to the O’ phase. Conversely, at a cutoff voltage of 4.1 V, the P3 and O3 phases with high sodium removal demonstrate excellent cycling stability. The specific capacities before and after 150 cycles (at 0.5C) are 142.3 and 113.7 mAh/g, respectively, indicating a tolerable internal structural stress within these high sodium removal phases. This contrasts with the differentiated internal structural stresses generated by the P3, O3, and O’ phases during phase transitions at a cutoff voltage of 4.3 V. The research underscores the importance of regulating reversible crystal phases within the tolerance range of internal stress and avoiding irreversible crystal phases to enhance the cycling stability of cathode materials. These findings provide crucial insights for optimizing NNFMO cathode materials and hold significant implications for the design of high-performance, long-life sodium-ion batteries.