Sidewall defects play a key role in determining the efficiency of GaN-based micro-light emitting diodes (LEDs) for next generation display applications, but there still lacks direct observation of defects-related recombination at the affected area. In this Letter, we proposed a direct technique to investigate the recombination mechanism and size effect of sidewall defects for GaN blue micro-LEDs. The results show that mesa etching will produce stress release near the sidewall, which can reduce the quantum confinement Stark effect (QCSE) to improve the radiative recombination. Meanwhile, the defect-related non-radiative recombination generated by the sidewall defects plays a leading role under low-power injection. In addition, the effective area of the mesas affected by the sidewall defects can be directly observed according to the fluorescence lifetime imaging microscope (FLIM) characterization. For example, the effective area of the mesa with 80 µm is affected by 23% while the entire area of the mesa with 10 µm is almost all affected. This study provides guidance for the analysis and repair of sidewall defects to improve the quantum efficiency of micro-LEDs display at low current density.