Provided are a structure color of photonic crystals in which a new structure of a structure color of photonic crystals is provided so that a nanoimprint process can be performed and mass productivity is improved, a method of manufacturing thereof, and a manufacturing apparatus thereof. The method of manufacturing a structure color of photonic crystals includes: forming a plurality of basic element layers by using nanoimprinting, the plurality of basic element layers comprising a plurality of basic unit bodies each having a symmetrical cross-section and thin film connecting portions connecting the basic unit bodies! sequentially stacking the basic element layers! removing the thin film connecting portions by using etching; and determining whether the structure color of photonic crystals is completed, wherein, when it is determined that the structure color of photonic crystals is not completed, the forming, the stacking, and the removing are repeatedly performed.