Conducting polymers are promising electrode materials for electrochemical capacitors, but are suffered from poor cycling stability and relatively low capacitance. Herein, a hollow shell coated on polypyrrole (Ppy) nanowires is designed and constructed with the assistance of atomic layer deposition (ALD). Ppy nanowires are firstly deposited on flexible carbon cloth by electrodeposition, then a thin sacrificial layer of ZnO and a thin shell of TiO2 are deposited uniformly on the surfaces of the nanowires. After removing the ZnO layer, a nanogap between the Ppy core and TiO2 shell is formed thus generate a hollow core-shell Ppy-TiO2 (noted as PpyOTiO(2)) nanoarray. When tested as supercapacitor electrodes, the hollow core-shell nanostructure shows apparent higher capacitance and better cycling stability than the bare nanowires. Such enhancement is ascribed to the rational hollow structure design that provides enlarged surface areas and enhanced structure stability. Such hollow structure can be extended to other conducting polymers and electrodes for various electrochemical applications.