The present invention relates to an apparatus for massive manufacturing a hierarchical structure that can hierarchically form high performance micro units one a flexible substrate. For this purpose, an apparatus for manufacturing a hierarchical structure according to the present invention is provided to layer micro units provided on a dummy substrate that is made of a hard material on a target substrate that is made of a flexible material by releasing the micro units from the dummy substrate. The apparatus includes: a transfer stage flat-transferring the dummy substrate by supporting the same and a main roller rolling the target substrate by winding the same as the transfer stage proceeds and layering the micro unit of the dummy substrate on the target substrate.