A strategy is proposed for the synthesis of heterogeneous/homogeneous binary arrays via stepwise colloidal lithography, using ZnO and Ni as model materials. A series of controllable and specific binary arrays like pore/pillar, pore/pore, ring/triangle nanoparticle and ring/pore were designed and then fabricated. The periodicity of the binary array can be tuned by the size of the polystyrene spheres, the size and structure of each unit in the array can be selectively controlled by proper heat treatment, and the distance between the adjacent units of two arrays can be manipulated by the incidence angle of metal vapor flow. This study gives an effective guide to designing desired patterns of heterogeneous/homogeneous binary arrays and accurately determining their size and structure. Furthermore, this strategy allows two materials with different properties, such as magnetic, photonic, catalytic and semiconducting, to be assembled in one array with tunable arrangements, with potential applications in multi-function nanodevices.