We have proposed a new method for the multiplexed synthesis of heterogeneous nanostructures using a top-down fabricated nanowire heater array. Hydrothermally synthesized nanostructures can be grown only on the heated nanowire through nanoscale temperature control using a Joule heated nanowire. We have demonstrated the selective synthesis of zinc oxide (ZnO) nanowires and copper oxide (CuO) nanostructures, as well as their surface modification with noble metal nanoparticles, using a nanowire heater array. Furthermore, we could fabricate an array of heterogeneous nanostructures via Joule heating of individual nanowire heaters and changing of the precursor solutions in a sequential manner. We have formed a parallel array of palladium (Pd) coated ZnO nanowires and gold (Au) coated ZnO nanowires, as well as a parallel array of ZnO nanowires and CuO nanospikes, in the microscale region by using the developed method.