In order to obtain the dielectric assembly characteristics of nanowires in the conductive island microelectrode system, a comparative experiments of nanowire manipulation in both systems were conducted based on the planar microelectrode pairs and the conductive island microelectrode systems. The nanowire dielectric assembly models of the planar microelectrode pairs and the conductive island microelectrode systems were established respectively: The motion trajectory of the nanowires from the initial position to the final bridging onto the microgap under the two models was explored. And the nanowires subjected to dielectrophoretic forces, alternating current heat flow, and the electrokinetic behavior of cooperation between the two in a conductive island microelectrode system were analyzed. The conductive island microelectrode system has a strong dielectric capture effect on nanowires, and the addition of conductive islands can make better capture of nanowires to the microgap. Meanwhile, the dielectric assembly of nanowires is affected by frequency. When the frequency reaches the flip frequency, the microfluidic vortex generated above the microgap can transport nanowires in the far-field region to the assembly area, which makes the nanowires to be assembled to the microgap by the positive dielectrophoretic force.