Embodiments of the invention provide a manufacturing method of a GaN-based light emitting diode. The method comprises the following steps of forming an epitaxial lamination on a substrate; forming a current barrier layer pattern and a transparent conducting layer pattern on the epitaxial lamination; carrying out dry etching so that a part of N-type first semiconductor layer is exposed so as to form a table board; forming an insulation protection layer on the table board, carrying out electrode lithography on the insulation protection layer so as to form a first electrode opening and a second electrode opening, and forming a metal electrode in each electrode opening so as to form a light emitting diode. By using the manufacturing method of the GaN-based light emitting diode, through adjusting lithography of each structure and an etching sequence, in a total process flow, the lithography only needs to be performed for three times so that the light emitting diode which has a same structure with the structure of the light emitting diode obtained through using a routine technology is acquired; manufacturing time of the light emitting diode is shortened; and material cost and production cost are reduced.