The invention provides a preparation method for a micro circuit flexible circuit board based on a micro-nano imprinting technology. The preparation method comprises the steps of forming a first flexible material layer and a second flexible material layer on the two surfaces of a substrate separately, forming a first groove structure and a first hole site structure, and forming a second groove structure and a second hole site structure separately; forming first conductive structures in each first groove structure and the first hole site structure; forming through holes in the substrate; and forming second conductive circuits in each second groove structure, the second hole site structure and the through holes to form a two-side interconnecting circuit. According to the preparation method for the micro circuit flexible circuit board based on the micro-nano imprinting technology, the combination between the conventional circuit board and the IC technology is realized, so that the application of micro electronic products on the flexible circuit boards is possible; the conductive circuits are embedded, so that the reliability of the circuits is greatly improved; the circuits prepared by a printing process or an electroplating process can form metal layers of different thicknesses in the internal and on the surface of the grooves; and in addition, a roll-to-roll technology is adopted, and pore formation is realized in the metal layer depositing process, so that the technology can be simplified and the cost can be reduced.