Low light extraction efficiency (LEE) remains a critical bottleneck in the performance of contemporary micro-light-emitting diodes (micro-LEDs). This study presents an innovative approach to improve the LEE of Gallium nitride (GaN)-based thin-film flip-chip (TFFC) micro-LEDs by integrating an inclined sidewall with photonic crystals (PhCs). Three-dimensional finite-difference time-domain (FDTD) simulations reveal that the inclined sidewall design significantly increases the escape probability of light, thereby improving LEE. Additionally, the PhCs’ structure further improves LEE by enabling more light to propagate into the escape cones through diffraction. Optimal results are achieved when the inclined sidewall angle (θ) is 28° and the PhCs exhibit a period (a) of 220 nm, a filling factor (f) of 0.8, and a depth (d) of 3 μm, resulting in a maximum LEE of 36.47%, substantially surpassing the LEE of conventional planar TFFC micro-LEDs. These results provide valuable design guidelines for the development of high-efficiency GaN-based micro-LEDs.