In this work, CuO samples with three different nanostructures, i.e., nanoflakes, nanoellipsoids, and nanorods, are successfully synthesized by a facile and environmentally friendly hydrothermal approach based on the use of different structure directing agents. The morphological influence on the anodic electrochemical performances, such as capacity, cycling stability, rate capability, and diffusion coefficient measurements of these different CuO nanostructures is comparatively investigated for sodium-ion batteries. The capacity and cycling stability are higher for the CuO nanorods (CuO-NRs) based electrode as compared to the cases of CuO nanoellipsoids (CuO-NEs) and CuO nanoflakes (CuO-NFs). At a low current density of 25 mA g-1, the CuO-NRs based electrode exhibits an excellent reversible capacity of 600 mA h g-1. It also exhibits a capacity of 206 mA h g-1 after 150 cycles with a capacity retention of 73% even at a higher current density of 1000 mA g-1. The exceptional performance of CuO-NRs is attributable to its slim nanorod morphology with a smaller particle size that provides a short diffusion path and the maximized surface area facilitating good diffusion in electrolytes, ensuring good electronic conductivity and cycling stability. The comparative analysis of these materials can provide valuable insights to design hierarchical nanostructures with distinct morphology to achieve better materials designed for sodium-ion batteries.