In this paper, we demonstrated the high performance GaN-based LEDs by using a high aspect ratio cone-shape nano-patterned sapphire substrate (HAR-NPSS). We utilized nano-imprint lithography (NIL) and dry-etching system to fabricate a high depth HAR-NPSS. The micro-scale patterned sapphire substrate (PSS) was also used for comparison. A great enhancement of light output was observed when GaN-based LEDs were grown on a HAR-NPSS or a PSS. The light output power of LEDs with a HAR-NPSS and LEDs with a PSS were enhanced of 49 and 38% compared to LEDs with a unpatterned sapphire substrate. The high output power of the LED with a HAR-NPSS indicated that the technology of NAR-NPSS not only can improve the crystalline quality of GaN-based LEDs but also a promising development to a NPSS.