Multiphase core-shell nanowires have been fabricated by controlling the ion transport processes of the microfluids in the nanochannels of the template. Both forced convection and pulsed potential induced migration can be applied to tune the morphologies of the nanostructures obtained by manipulating the ion transport during electrodeposition. The morphology and content of the core-shell structure were studied by field emission scanning electron microscope (FESEM) analysis, transmission electron microscope (TEM) analysis and energy dispersive spectrometry (EDS), respectively. The magnetic properties were analyzed by vibrating sample magnetometer (VSM) analysis. A magnetically hard core and soft shell constitutes the multiphase composite nanostructure. The unique magnetic hysteresis curve indicates the decoupled magnetic reversal processes of the two components. Our work provides deeper insights into the formation mechanisms of a new core-shell nanostructure, which may have potential applications in novel spintronics devices.