A new and universal synthetic strategy to hybridize metal oxides and conduct polymer nanocomposites has been proposed in this work. The simultaneous reaction process, which includes the generation of metal oxide layers, the oxidation polymerization of monomers, and the in situ formation of polymer–metal oxides sandwich structure is successfully realized and results in the unique hybrid polyaniline (PANI)-intercalated molybdenum oxide nanocomposites. The peroxomolybdate proved to play a dual role as the precursor of the inorganic hosts and the oxidizing agent for polymerization. The as-obtained hybrid nanocomposites present a flexible lamellar structure by oriented assembly of conductive PANI chains in the MoO3 interlayer, and thus inherit excellent electrical performance and possess the potential of active electrode materials for electrochemical energy storage. Such uniform lamellar structure together with the anticipated high conductivity of the hybrid PANI/MoO3 nanocomposites afford high specific capacitance and good stability during the charge–discharge cycling for supercapacitor application.