The invention discloses a nanoimprint based preparation method of a GaN (Gallium Nitride)-based LED, comprising the following steps of: (1) preparing a nanoimprint template by utilizing an aluminum anodic oxidation method; (2) carrying out antisticking treatment on the nanoimprint template; (3) rotationally coating a layer of photoresist on a target chip; (4) carrying out nanoimprint on the nanoimprint template and the target chip; (5) separating the nanoimprint template subjected to nanoimprint treatment from the target chip so as to form needed patterns on the photoresist positioned on the surface layer of the target chip; (6) transferring the patterns to the target chip by utilizing ICP (Inductively Coupled Plasma) etching or RIE (Reactive Ion Etching) etching; and (7) carrying out subsequent process treatment on the target chip to prepare the GaN-based LED. The preparation method is simple, convenient and easy to operate and can be used for preparing the nanoimprint template through the anodic oxidation method and manufacturing the GaN-based photonic crystal LED with high light-emitting efficiency through a nanoimprint technology suitable for large-scale industrial production.