Traditional optical lithography techniques to fabricate three-dimensional (3D) nanostructures are complicated and time consuming. Due to the capability to replicate nanostructures repeatedly in a large area with high resolution and uniformity, nanoimprint (NI) has been recognized as one of the promising approaches to fabricate 3-D nanostructures with high throughput and low cost. This paper introduces a novel 3-D nanostructure fabrication method by nanoimprint on silicon substrate. Nanoscale gratings and microlens array are taken as examples of 3-D nanostructures fabricated by nanoimprint. High fidelity demonstrates the possibility of nanoimprint to fabricate 3-D nanostructures on silicon substrate.