ZnO 3D hierarchical structures (3DHNs) with different morphologies have been selectively synthesized at room temperature by using potassium hydroxide (KOH) and citric acid (CA) as an etchant and capping agent, respectively. A possible formation mechanism based on capping–etching competitive interactions has been proposed for the formation of distinct ZnO 3DHNs under different growth conditions. The photocatalytic performance for the degradation of organic contaminants can be improved by fine tuning the morphology of the 3DHNs.