Sodium ion batteries (SIBs) are considered a potential energy storage technology due to their low cost and the abundance of sodium resources. Numerous strategies have been made to address the remaining challenges such as low electronic conductivity, huge volume change, and sluggish sodium ions kinetics. In spite of impressive advances, a comprehensive understanding of the microstructure-stability correlation remains elusive. Here, the three-dimensional (3D) Fe3S4 flower-like hierarchical materials constructed from two-dimensional (2D) nanosheet building units were synthesized via a facile and cost-effective method. Instead of materials synthesis and performance evaluation, more attentions have been paid on the underlying coupling mechanism between microstructure design, surface chemistry and 3D electronic/ionic transport pathways. It found that the thin and stable SEI layer generated by ether-based electrolytes contributes to the stable surface chemistry and fast interfacial Na+ ion transport, while 3D hierarchical structure enables short diffusion distance, volume change accomodation as well as stabilizing SEI layer. Taking advantage of the inherent high electronic conductivity in Fe3S4, we have demonstrated the paramount importance of the synergistic strategy to improve the stability of SIBs through X-ray nanotomography. This work explicitly illuminate the electrochemical stability mechanisms of 3D hierarchitectures and resolves new strategies to rational design SIBs anodes.