In this work, local nanotip arrays on GaN-based light-emitting (LED) structures were fabricated through nano-oxidation using an atomic force microscope (AFM). The photoluminescence (PL) intensity of the InGaN/GaN multiple quantum wells (MQWs) active layer and the light extraction efficiency of the LED structure were enhanced by forming this nanotips structure to serve as a graded-refractive index layer, which is further validated by the finite-difference time-domain analysis. The PL emission peak of the MQWs active layer has a blue-shift phenomenon that is caused by a partial reduction of the strain on the InGaN well. It is expected that our approach opens a promising route for simultaneously enhancing both the internal quantum efficiency and the light extraction efficiency of GaN-based LEDs. The proposed AFM-based method will be of importance for local patterning the light emitting components for optoelectronic applications.