The present invention relates to a three-dimensional nanostructure, and a preparation method thereof, and more specifically, to various shapes of three-dimensional nanostructures having a large area, a high aspect ratio and uniformity prepared by forming an objective material-polymer composite structure in which an objective material is adhered to the outer circumferential surface of a patterned polymer structure by applying ion bombardment through a physical ion etching process, and removing the polymer of the objective material-polymer composite structure, and a preparation method thereof. According to the present invention, the preparation method of a three-dimensional nanostructure can prepare a three-dimensional nanostructure having a high aspect ratio and uniformity through a simple low cost process by applying ion bombardment through a physical ion etching process, and can easily prepare various shapes of structures and can form a uniform nanostructure having a large area and a thickness of 10 nm or less by controlling the pattern and shape of a polymer structure at the same time. Therefore, it is possible to implement the high performance of a future nano-device such as a nano electronic device, an optical device, a bio-device, an energy device, and the like.