High capacity transition metal oxides have attracted much attention as potential sodium-ion batteries (SIBs) anodes. However, the fast capacity fading greatly limits their practical applications. In this study, highly crystallized mesoporous Fe3O4 nanoparticles encapsulated in the hollow nitrogen-doped carbon nanospheres (denoted as HCM-Fe3O4@void@N-C) have been synthesized and then explored as anode materials for SIBs. The resultant HCM-Fe3O4@void@N-C nanospheres possess a uniform particle size of ~ 180 nm with highly crystallized mesoporous Fe3O4 cores (~ 100 nm in diameter), a large surface area of ~ 250 m2 g−1 and a nitrogen-doped carbon shell (~ 7.6 wt%). Notably, a high discharge capacity of 372 mA h g−1 is obtained after the first five cycles at 160 mA g−1, which can gradually increase and be maintained at an ultrahigh specific capacity of 522 mA h g−1 even after 800 cycles. Besides, remarkable rate performance with a capacity of 196 mA h g−1 at a current density of 1200 mA g–1 and a high Coulombic efficiency (~ 100%) are obtained. Such good performance can be attributed to the unique yolk-shell nanostructure with a high crystallized mesoporous Fe3O4 core, a high conductive N-doped carbon shell, and a suitable void space, paving a new way to design and synthesize high-performance anode materials for SIBs.