In this paper, we demonstrate a novel method to integrate photonic crystals (PhCs) on GaN-based blue light-emitting diodes (LEDs) using a silicon substrate as a mold for forming the PhCs. This method starts with fabricating a 2D grooved Si substrate as that mold. Subsequently, GaN-based epitaxial layers are grown on the Si mold-substrate, which effectively reduces the dislocation density in GaN by enhanced lateral epitaxial growth. After the epitaxial layers are bonded onto a highly reflective substrate, the Si mold-substrate is removed. This substrate-transfer technique replicates PhC from the mold-substrate on the LED surface free from processing damages. The resultant LEDs with PhC have outperformed the LEDs without PhC in the optical output power by 80%, taking advantage of the enhanced light extraction by PhC.