The invention relates to a preparation method of a sub-micron-sized two-dimensional dielectric cylindrical photonic crystal, and the preparation method comprises: depositing Si3N4 by plasma-enhanced chemical vapor deposition (PECVD), carrying out spin coating, soft baking and vertical crossover exposure, baking after exposure, developing step by step, etching Si3N4 by reactive ion etching (RIE), removing the photoresist, etching the substrate material by inductively coupled plasma etching (ICP) and removing Si3N4. Through the preparation method, the problem that the two-dimensional dielectric cylindrical photonic crystal is difficult to prepare by using a positive photoresist in holographic interferometry is solved. Compared with electron beam exposure and other methods, the preparation method has the advantages of simplicity in operation, low price, precise control, large-area preparation and the like, meets the need of the preparation of the sub-micron-sized two-dimensional dielectric cylindrical photonic crystal and has good application prospects.