ZnO/Si nanowire arrays with hierarchical architecture were synthesized by solution method with ZnO seed layer grown by atomic layer deposition and magnetron sputtering, respectively. The photocatalytic activity of the as-grown tree-like arrays was evaluated by the degradation of methylene blue under ultraviolet light at ambient temperature. The comparison of morphology, crystal structure, optical properties, and photocatalysis efficiency of the two samples in different seeding processes was conducted. It was found that the ZnO/Si nanowire arrays presented a larger surface area with better crystalline and more uniform ZnO branches on the whole sidewall of Si backbones for the seed layer by atomic layer deposition, which gained a strong light absorption as high as 98% in the ultraviolet and visible range. The samples were proven to have a potential use in photocatalyst, but suffered from photodissolution and memory effect. The mechanism of the photocatalysis was analyzed, and the stability and recycling ability were also evaluated and enhanced.Electronic supplementary materialThe online version of this article (doi:10.1186/s11671-016-1803-0) contains supplementary material, which is available to authorized users.