Indium tin oxide (ITO)/ indium oxide (InxO) double layer structure was adopted as the transparent conduction and light scattering function layer to improve the light extraction efficiency of the GaN-based blue LEDs. The double layer structure was first deposited in one run by electron beam evaporation using ITO and Indium as the source respectively, and then annealed in an oxygen environment. This method can fabricate transparent electrode with microstructure and low specific contact resistivity one time free from lithography and etching, which makes the fabrication process simple and at a ower cost. For the 220 nm ITO/ 170 nm InxO double layer sample annealed at 600°C for 15 min in oxygen, measurement results show that its root mean square of roughness of the surface microstructure can be as high as 85.2 nm which introduces the strongest light scattering. Its light transmittance at 450 nm can maintain 92.4%. At the same time, it can realize lower specific contact resistivity with p-InGaN. Compared with the GaN-based blue LEDs with only 220 nm ITO electrode, the light output power of the LEDs with 220 nm ITO/ 170 nm InxO double layer structure can be increased about 58.8%, and working voltage at 20 mA injection current is decreased about 0.23 V due to the enhanced current spreading capability. The light output power improvement is also theoretically convinced by finite difference time domain simulations.