Problems of low initial Coulombic efficiency and low cycling life are main limitation factors for SnO2-based materials in sodium storage application. Herein, a cobalt-doped SnO2/carbon cluster is prepared via a simple and fast microwave assisted hydrothermal method. It reveals an iconic hierarchical structure including SnO2 nanoparticles and whiskers, to be demonstrated with excellent electrochemical performance in sodium storage application. In details, a high specific capacity of 576 mAh g−1 can be obtained at a current density of 50 mA g−1 after 250 cycles; an impressive rate capacity of 242 mAh g−1 can be obtained even at a high current density of 1600 mA g−1. It is found that the cobalt dopant can inhibit the SnO2 coarsening, increase the overall conductivity and improve the reversibility of conversion reactions of Sn to SnO2. As a result the as-prepared cobalt-doped SnO2/carbon cluster presents a high initial Coulombic efficiency and an enhanced Na+ diffusion rate, corresponding to high specific capacity and excellent rate performance in sodium storage application. This work demonstrated a promising technique to prepared cobalt-doped nanostructured SnO2/carbon nanocomposites with excellent electrochemical performance as anode for sodium storage application.