We develop a novel multi-level nanoimprinting mold fabrication methodology realizing the uniform pattern height of each level with the deviation less than 2.6%, by applying the unique ‘top-to-bottom’ level patterning protocol in contrast to typical bottom-to-top patterning sequence. This is implemented by performing sequential dry etching of the stack of etch stop layers and organic insulation layers of desired thicknesses, with proper photolithographic masking in between. We demonstrate that the fabrication can be conducted on a flexible substrate without deformation of pattern profile, which then can be utilized in continuous roll-to-roll nanoimprinting of multi-level nanoarchitectures in a single imprinting process without resorting to alignment of each level. Many applications will benefit from our method, particularly requiring large-area multi-level nanoarchitectures such as thin-film transistor arrays in flexible displays.