SnO2 nanowires directly grown on flexible substrates can be a good electrode for a lithium ion battery. However, Sn-based (metal Sn or SnO2) anode materials always suffer from poor stability due to a large volume expansion during cycling. In this work, we utilize atomic layer deposition (ALD) to surface engineer SnO2 nanowires, resulting in a new type of hollowed SnO2-in-TiO2 wire-in-tube nanostructure. This structure has radically improved rate capability and cycling stability compared to both bare SnO2 nanowires and solid SnO2@TiO2 core-shell nanowire electrodes. Typically a relatively stable capacity of 393.3 mAh/g has been achieved after 1000 charge-discharge cycles at a current density of 400 mA/g, and 241.2 mAh/g at 3200 mA/g. It is believed that the uniform hollow TiO2 shell provides stable surface protection and the appropriate-sized gap effectively accommodates the expansion of the interior SnO2 nanowire. This ALD-enabled method should be general to many other battery anode and cathode materials, providing a new and highly reproducible and controllable technique for improving battery performance.