GaN-based micro-size light-emitting diode (μLED) have emerged as a promising light sources for a wide range of applications in displays, visible light communication etc. In parallel with the two key technological bottlenecks: full-color scheme and mass transfer technique that need overcoming, it is known that the low external quantum efficiency (EQE) is also another challenge for μLEDs from the perspective of manufacturing technology and device physics. The low EQE for GaN based μLEDs is opposite to the common belief for GaN-based LEDs, such that GaN based LEDs are featured with high quantum efficiency, mechanically robust and energy saving. Therefore, in this work, we have reviewed the origin for the low EQE for μLEDs. More importantly, we have also reported the underlying devices physics and proposed optimization strategies to boost the EQE for μLEDs. Our work is targeted to provide a guideline for the community to develop high-performance GaN-based μLEDs.