We develop a novel way to fabricate subwavelength nanostructures on the freestanding GaN slab using a GaN-on-silicon system by combining selfassemble technique and backside thinning method. Silicon substrate beneath the GaN slab is removed by bulk silicon micromachining, generating the freestanding GaN slab and eliminating silicon absorption of the emitted light. Fast atom beam (FAB) etching is conducted to thin the freestanding GaN slab from the backside, reducing the number of confined modes inside the GaN slab. With self-assembled silica nanospheres acting as an etching mask, subwavelength nanostructures are realized on the GaN surface by FAB etching. The reflection losses at the GaN interfaces are thus suppressed, When the InGaN/GaN multiple quantum wells (MQWs) active layers are excited, the light extraction efficiency is significantly improved for the freestanding nanostructured GaN slab. This work provides a very practical approach to fabricate freestanding nanostructures on the GaN-on-silicon system for further improving the light extraction efficiency.