Alloy-based nanostructure anodes have the privilege of alleviating the challenges of large volume expansion and improving the cycling stability and rate performance for high energy lithium- and sodium-ion batteries (LIBs and SIBs). Yet, they face the dilemma of worsening the parasitic reactions at the electrode-electrolyte interface and low packing density for the fabrication of practical electrodes. Here, pomegranate Sb@C yolk-shell microspheres were developed as a high-performance anode for LIBs and SIBs with controlled interfacial properties and enhanced packing density. Although the same yolk-shell nanostructure (primary particle size, porosity) and three-dimensional architecture alleviated the volume change induced stress and swelling in both batteries, the SIBs show 99% capacity retention over 200 cycles, much better than the 78% capacity retention of the LIBs. The comparative electrochemical study and X-ray photoelectron spectroscopy characterization revealed that the different SEIs, besides the distinct phase transition mechanism, played a critical role in the divergent cycling performance.