A GaN-based LED and a method for manufacturing the same are provided, and the method includes: providing a substrate, depositing a first transition layer on the substrate; forming a first patterned transition layer by etching with a mask; growing a first epitaxial layer on the first patterned transition layer; depositing a second transition layer on the first epitaxial layer; forming a second patterned transition layer by etching with a mask, such that the second patterned transition layer and the first patterned transition layer are cross-staggered with each other; growing a second epitaxial layer on the second patterned transition layer, wherein the second epitaxial layer includes a P-type layer, a light-emitting layer and an N-type layer; depositing a protection layer on the second epitaxial layer, dicing to obtain chips with a defined size; removing the first patterned transition layer and the second patterned transition layer on the substrate and the protection layer on the second epitaxial layer by wet etching, so as to form a structure with two layers of cross-staggered through holes; forming a conductive layer on the second epitaxial layer; and forming a P-electrode and an N-electrode by etching with a mask. The two layers of cross-staggered through holes of the LED chips can effectively reduce the dislocation density in the epitaxial growth of the GaN-based layer, and improve the lattice quality and luminous efficiency.