The cobalt-substituted tin dioxide nanocrystals were synthesized by the one-pot hydrothermal method. According to the powder X-ray diffraction and elemental analyses, the cobalt ions were successfully substituted into the rutile lattice of the SnO2 phase, which consequently resulted in an increase in the volume of the unit cell. Electron microscopy revealed that with an increase in the content of the substituted cobalt ions, the particle size of the SnO2 nanocrystals becomes smaller. In addition, the X-ray absorption spectroscopy clearly demonstrated that the substituent cobalt ions were stabilized in a divalent oxidation state in a distorted octahedral symmetry, while the tin ions were in a tetravalent oxidation state. The electrochemical measurements revealed that the substitution of Sn with Co significantly enhanced the negative electrode performance of tin dioxide nanocrystals at optimal Co content. The present study clearly demonstrated that a partial substitution of cobalt in the SnO2 phase can provide an effective way of optimizing the electrochemical properties of the tin dioxide nanocrystals.