Two-dimensional (2D) nanostructures, though promising in energy storage, suffer from aggregation and subsequent deterioration of performance in practical applications. Hence, assembly of 2D nanostructures into three-dimensional (3D) architectures is highly desirable. Here, we report a microwave-assisted approach to the controllable synthesis of 2D materials with tunable 3D structures simply by adjusting the ratio of water/ethylene glycol (H2O/EG). Novel flower-on-sheet 3D hierarchical structures of nickel cobalt double hydroxide (NiCo LDHs) are obtained at EG content of 40%, while microspheres and 2D nanosheets are obtained when the EG content is 0% and 75%, respectively. We propose that under microwave irradiation, EG molecules disperse the nuclei and facilitate the initial formation of 2D sheets. Subsequently, the dominating hydrophobicity of the assembling results in the formation of nanoflowers on the sheets. When tested as electrode materials in supercapacitors, the flower-on-sheet NiCo LDH exhibits superior capacitance (1187.2 F g−1 at 1 A g−1), good rate capability (71% retention at 30 A g−1), and high stability (only 0.3% cyclic decay per cycle with respect to the first charge capacitance), which is ascribed to that ‘sheet’ could act as buffer substrate while ‘flower’ expose more active site. Our results demonstrate an energy-saving and one-pot approach for controllable construction of 2D derived 3D nanostructure that can be applied in next-generation energy storage materials.