Tin dioxide (SnO2) is a promising alternative material to graphite anode, but the large volume change induced electrode pulverization issue has limited its application in lithium-ion batteries (LIBs). In contrast, titanium dioxide (TiO2) anode shows high structure stability upon lithium insertion/extraction, but with low specific capacity. To overcome their inherent disadvantages, combination of SnO2 with TiO2 and highly conductive carbon material is an effective way. Herein, we report a facile fabrication method of carbon-coated SnO2/TiO2 nanowires (SnO2/TiO2@C) using tin titanate nanowires as precursor, which are prepared by reacting SnCl2·2H2O with layered sodium titanate (Na2Ti3O7) nanowires in the aqueous solution though the ion exchange between Sn2+ and Na+. After annealing under argon atmosphere, the hydrothermally carbon-coated tin-titanate nanowires decompose, forming a unique hybrid structure, where ultrafine SnO2 nanoparticles are uniformly embedded within the TiO2 substrate with carbon coating. Consequently, the SnO2/TiO2@C nanowires demonstrate excellent lithium storage capacity with high pseudocapacitance contribution, excellent reversible capacity, and long-term cycling stability (673.7/510.5 mAh/g at 0.5/1.0 A/g after 250/800 cycles), owing to the unique hybrid structure, as the well-dispersion of ultra-small SnO2 within TiO2 nanowire substrate with simultaneous carbon coating efficiently suppresses the volume changes of SnO2, provides abundant reactive sites for lithium storage, and enhances the electrical conductivity with shortened ion transport distance.