The invention discloses a method for preparing a multilayer unequal-height micro-nano structure used in a flexible structure. The method comprises the following steps: classifying a to-be-prepared unequal-height micro-nano structure according to structural height; preparing a micro-nano structure part with the lowest height through replication of a silicon template via PDMS; and successively carrying out transfer-process preparation on the rest micro-nano structure parts used as to-be-transferred PDMS structures according to a sequence from lower height to higher height by using a high-shape-maintenance transfer process until a micro-nano structure part with the highest height is prepared. The method provided by the invention prepares the multilayer unequal-height micro-nano structure by transferring a mono-layer structure onto a basic structure layer by layer; and the method is simple in process, easy to realize integration of the micro-nano structure parts and extensively applicable to manufacturing of a bionic multilayer micro-nano structure and a super-hydrophobic structure.