Abstract2D layered embedding materials have shown promising applications in rapidly rechargeable sodium‐ion batteries (SIBs). However, the most commonly used embedding structures are susceptible to damage and collapse with increasing cycles, which in turn leads to a degradation of the overall performance of the batteries. In order to address this issue, a “stress‐strain transition” mechanism is proposed to form a heterostructure by introducing pyramid‐like MnSe into the MoS2 lattice to reduce the irreversible reconstruction under deep discharge. Density functional theory and Finite element method simulation reveal that the strong orbital coupling of Mn–Mo at the heterogeneous interface provides a guarantee for the directional migration of ions, alleviates the lattice expansion caused by embedding strain, and avoids irreversible structural changes during battery operation. The capacity measured at 0.1C is 612 mAh g−1, which is consistent with the theoretical prediction. The experimental results demonstrate that the capacity is maintained at 80.3% of the initial value after 3500 cycles. This work demonstrates a strategy of addressing the structural collapse of 2D layered materials and paves the way for the commercialization of SIBs.