A new well-aligned cone-shaped nanostructure of polypyrrole (WACNP) has been successfully grown on Au substrate by using a simple, one-step, reliable, and template-free anodic deposition method. The formation mechanism of WACNP is proposed, in which the hydrogen bonding introduced from phosphate buffer solution (PBS) promotes the formation of a well-aligned nanostructure of polypyrrole (PPy), while the steric hindrance effect arisen from high concentration of pyrrole (Py) boosts its vertical alignment and further forms a cone-shaped nanostructure. The 3D, arrayed, nanotubular architecture coated with an ultrathin layer of RuO2 by the magnetron sputtering deposition method was tailored to construct a supercapacitor. The unique structure and design not only reduces the diffusion resistance of electrolytes in the electrode material but also enhances its electrochemical performance. The modification of RuO2 on WACNP results in a capacitance higher than that of WACNP by three times. The specific capacitance of RuO2/WACNP is 15.1 mF cm−2 (302 F g−1) measured by the charge−discharge method with an applied current density of 0.5 mA cm−2 over a potential range of −0.2 to 0.7 V, and is greater than that of commercial carbon materials by 2−3 orders of magnitude. The high capacitance and good stability of the RuO2/WACNP electrode is very promising for applications in microsupercapacitor devices.