Uniquely structured Fe2O3 and FeSe2/graphitic-carbon (GC) microrods composed of hollow Fe2O3 and FeSe2 nanospheres, respectively, were successfully prepared by applying a metal-organic framework (MOF, MIL-88) as the precursor and template. This strategy involves the fabrication of Fe@GC microrods by the thermal reduction of MIL-88 microrods followed by transformation into hollow Fe2O3 nanosphere aggregate (H-Fe2O3-NSA) microrods and hollow FeSe2 nanosphere aggregate/GC (H-FeSe2/GC) microrods by means of oxidation and selenization, respectively. During the post-treatment step, metallic Fe nanocrystals embedded in GC are converted into hollow metal compound nanospheres through nanoscale Kirkendall diffusion. This novel structure makes it possible to achieve a superior electrochemical performance by alleviating the volume variation and providing ample ion reaction sites. In addition, in the case of H-FeSe2/GC, the carbon framework not only prevents the structural collapse but also ensures sufficient electron transport during repeated cycles. Thus, the H-Fe2O3-NSA and H-FeSe2/GC microrods have high specific discharge capacities of 973 mA h g(-1) after 400 cycles at 1 A g(-1) and 587 mA h g(-1) after 100 cycles at 0.2 A g(-1) when applied as anode materials for lithium-ion and sodium-ion batteries, respectively.