3D networked polypyrrole (PPy) nanotube/N-doped graphene (NDG) has been fabricated through a facile two-step method, in-situ polymerization assisted by MoO3 template and a microwave-assisted hydrothermal method at a short time. The MoO3 template-assisted polymerization is demonstrated as an effective way to obtain PPy nanotubes with controlled thickness. It is found that the PPy nanotube formation and N doping of reduced graphene oxide occur simultaneously during the microwave process at short time. Due to the unique structure and excellent electrical conductivity, the PPy nanotube/NDG shows extremely small equivalent series resistance of 1.7 Ω, charge transfer resistance (Rc) of 0.1 Ω, pore resistance (Rd) of 0.1 Ω, and specific capacitance (Csp) of 292 F g−1 at 5 mV s−1. Also, a novel MoS2-decorated core-shelled MoO3/PPy has also been fabricated through a facile method. Owing to the unique structure and rich redox activities, MoS2-decorated core-shelled MoO3/PPy shows excellent performance with Csp of 527 F g−1 at 5 mV s−1 and low charge transfer resistance of 0.5 Ω. Furthermore, an aqueous asymmetric supercapacitor, consisting of MoS2/MoO3/PPy positive electrode and PPy nanotube/NDG negative electrode, has been constructed. The asymmetric supercapacitor shows an excellent energy density of 43.2 Wh kg−1 at power density of 674 W kg−1. The asymmetric supercapacitor also shows an excellent retention of 126% after 5000 cycles, possess high potential for application in the energy storage.