Zinc oxide (ZnO) is a wide-band-gap semiconductor that is promising for use as a transparent conductive oxide film. To date, to improve their optoelectrical properties, pristine ZnO films have been doped with metals using various techniques. In this study, nanostructured Cu-ZnO thin films were synthesized using a modified two-step radio frequency magnetron sputtering technique with separate ZnO and metallic Cu targets. Controlling the timing of the Cu/ZnO co-sputtering and ZnO-only sputtering steps afforded a significant change in the resulting nanostructures, such as uniform Cu-ZnO and broccoli-structured Cu-ZnO thin films. Using various measurement techniques, the influence of Cu doping was analyzed in detail. Furthermore, a crystal growth model for the formation of the broccoli-like clusters was suggested. The Cu-ZnO thin films synthesized using this technique demonstrate a highly improved conductivity with some loss in optical transmittance.