Three-dimensional (3D) metal oxide superstructures have demonstrated great potentials for structure-dependent energy storage and conversion applications. Here, we reported a facile hydrothermal method for direct growth of highly ordered single crystalline nanowire array assembled 3D orthorhombic Nb3O7(OH) superstructures and their subsequent thermal transformation into monoclinic Nb2O5 with well preserved 3D nanowire superstructures. The performance of resultant 3D Nb3O7(OH) and Nb2O5 superstructures differed remarkably when used for energy conversion and storage applications. The thermally converted Nb2O5 superstructures as anode material of lithium-ion batteries (LiBs) showed higher capacity and excellent cycling stability compared to the Nb3O7(OH) superstructures, while directly hydrothermal grown Nb3O7(OH) nanowire superstructure film on FTO substrate as photoanode of dye-sensitized solar cells (DSSCs) without the need for further calcination exhibited an overall light conversion efficiency of 6.38%, higher than that (5.87%) of DSSCs made from the thermally converted Nb2O5 film. The high energy application performance of the niobium-based nanowire superstructures with different chemical compositions can be attributed to their large surface area, superior electron transport property, and high light utilization efficiency resulting from a 3D superstructure, high crystallinity, and large sizes. The formation process of 3D nanowire superstructures before and after thermal treatment was investigated and discussed based on our theoretical and experimental results.