As the diminution of micro-LED pixels advances, the pivotal role of dislocation phenomena becomes increasingly pronounced. This study provides insight into the key characteristics and dominant mechanisms of GaN-based micro-LEDs by comparing the homoepitaxial and heteroepitaxial configurations. Our findings reveal that variability in V-shaped pits distribution markedly influences the performance and uniformity of micro-LED chips. While the homoepitaxial micro-LEDs, alongside significantly reduced dislocation density and residual stress, effectively preclude the formation of them and thus ensuring superior uniformity both within and among micro-LED chips. Notably, the external quantum efficiency (EQE) peak of homoepitaxial micro-LEDs surpasses that of heteroepitaxial variants by 40%. Motivated by the realization that the reduced MQW thickness at the sidewalls of V-shaped pit aids carrier injection, a great enhancement in EQE from 7.9% to 14.8% (@ 10 A/cm2) was achieved by the optimization of homoepitaxial structure. Therefore, the growth of micro-LED with lower dislocation density, lower residual stress, and epi-structure of low-energy-barrier MQWs demonstrated the profound impact on advancing micro-LED technology to obtain the performance of high uniformity, high brightness, and low power consumption.