N-polar GaN etching process and mechanism has been investigated in detail by varying the etching parameter (etchant temperature, etchant concentration, and etching duration) in KOH and H3PO4. Quasi-perfect micro-scale hexagonal pyramids vertical light emitting diodes (μ-HP VLEDs) array with least active area loss (<12%) has been fabricated by N-polar etching. The μ-HP VLEDs shows massively improved crystal quality with X-ray diffraction full width at half maxima decreased from 442 s to 273 s, and the room temperature minority carriers decay time increased from 252 ps to 747 ps. Temperature dependence of photoluminescence result reveals a ∼30% improved internal quantum efficiency, and transmission electron microscope further reveals its quasi-perfect crystalline quality clearly.