We report a method for synthesizing three distinct type II 3D ZnO/ZnSe heterostructures through simple solution-based surface modification reactions in which polycrystalline ZnSe nanoparticles formed on the surfaces of single-crystalline ZnO building blocks of 3D superstructures. The experimental results suggested a possible formation mechanism for these heterostructures. The formation of the ZnO/ZnSe heterostructures was assumed to result from a dissolution-recrystallization mechanism. The optical properties of the 3D ZnO/ZnSe heterostructures were probed by UV-vis diffuse reflectance spectroscopy. The 3D ZnO/ZnSe heterostructures exhibited absorption in the visible spectral region. The visible photocatalytic activities of 3D ZnO/ZnSe heterostructures were much higher than those of the 3D pure ZnO structures. The activities of the 3D ZnO/ZnSe heterostructures varied according to the structures under visible light. The morphologies and exposed crystal faces of pure ZnO building blocks prior to surface modification had a significant effect on the visible light photocatalytic processes of ZnO/ZnSe heterostructures after surface modification.