We studied a new approach where structurally gradient nanostructures were fabricated by means of hydrodynamics. Zinc oxide (ZnO) nanorods were synthesized in a drag-driven rotational flow in a controlled manner. The structural characteristics of nanorods such as orientation and diameter were determined by momentum and mass transfer at the substrate surface. The nucleation of ZnO was induced by shear stress which plays a key role in determining the orientation of ZnO nanorods. The nucleation and growth of such nanostructures were modeled theoretically and analyzed numerically to understand the underlying physics of the fabrication of nanostructures controlled by hydrodynamics. The findings demonstrated that the precise control of momentum and mass transfer enabled the formation of ZnO nanorods with a structural gradient in diameter and orientation.