This study presents a general approach for the synthesis of carbon-encapsulated wire-in-tube Co3O4/MnO2 heterostructure nanofibers (Co3O4/MnO2@C) via electrospinning followed by calcination. The as-synthesized Co3O4/MnO2@C is investigated as the sodium-ion batteries anode material, which not only exhibits a high reversible capacity of 306 mAh g(-1) at 100 mA g(-1) over 200 cycles, but also shows a cycling stability of 126 mAh g(-1) after 1000 cycles at a high current density of 800 mA g(-1). The excellent electrochemical performance can be ascribed to the contribution from carbon-encapsulated outer-tube Co3O4 and inner-wire MnO2 heterostructures, which offer a large internal space and good electrical conductivity. The present work can be helpful in providing new insights into heterostructures for sodium-ion batteries and other applications.