The rate of photo-electro-chemical (PEC) etching on N-polar n-GaN using vertical light emitting diodes (V-LEDs) has been investigated in detail, by varying the etching parameters (etchant concentration, etching duration and light intensity). V-LED with optimal hexagonal pyramid structure (the side-wall angle is 31°) has been fabricated, and then the influence of the PEC etching on the electrical and optical properties of V-LED has been analyzed. After PEC etching, the sample has good ohmic contact with the electrode and has lower contact resistance than a reference sample. The electrical characteristics have a better improvement. And the light output power has improved obviously after PEC etching, which shows 86.1% enhancement at 20 mA. Effect of side-wall angle of the pyramids on light extraction efficiency (LEE) in V-LEDs is theoretically calculated by finite difference time domain (FDTD) method. Simulation results show that the LEE is significantly increased for the sidewall angle between 20° and 40°, and the maximum enhancement is realized at a side-wall angle of 23.6° (the total reflection angle at the GaN/air interface).