The GaN-based light emitting diodes (LEDs) were grown on the cone-shaped patterned sapphire substrates (PSSs) by metal-organic chemical vapor deposition. To enhance the epilayer quality and optoelectronic performance of LEDs, the PSSs were further wet etched to form the modified top-tip cone shapes. After the wet etching process, some dry-etched induced damage on sapphire surface generated in the PSS fabrication process could be removed, leading to a higher crystal quality in epilayer and better device performance. As the wet etching time was increased to 3 min, the LED grown on the cone-shaped PSS had 53% and 8% improvement in light output (@ 20 mA) compared to that on conventional sapphire substrate (CSS) and the cone-shaped PSS without wet etching, respectively. It indicates that the technique of the modification in PSS shape has a high potential in LEDs application.