This paper reports a novel process which is combine the contact metal transfer method and traditional photolithography process for fabricate nano-scale pattern sapphire substrate (NPSS) used in high brightness light emitting diodes (LEDs). The novel process can directly transfer a metal pattern onto the PR layer which above the sapphire substrate, the transferred metal pattern can as a perfect photo-mask for subsequent photolithography process. In this work, the high aspect ratio PR structures with the aspect ratio of 5 and line width of 500 nm are created by this novel process. Furthermore, the PR structure can as a etching mask for inductively coupled plasma (ICP) etching on the sapphire substrate. During the ICP etching, we successfully to obtain the NPSS with a perfect cone shape. Experiments have been demonstrate the feasibility of using this new approach for obtaining sub-micrometer surface structures on the complete surface area of a 2 inch and 4 inch sapphire substrates.