GaInN/GaN multi-quantum-shell (MQS) nanowires (NWs) are gaining increasing attention as promising materials for developing highly efficient long-wavelength micro-light emitting diodes (LEDs). To improve the emission properties in GaInN/GaN MQS NWs, it is necessary to suppress the emission from the (0001) c-plane MQS at the apex region, which featured with low crystalline quality. In this study, we investigated the enhancement of optical properties and the realization of micro-LEDs by confirming the effect of the (0001) plane region. A 7.9-fold enhancement of the electroluminescence (EL) intensity was demonstrated by removal the (0001) plane region via inductively coupled plasma (ICP) dry etching, owing to the promoted current injection into the (1–101) semi-polar and (10–10) non-polar sidewall area. To investigate the effect of the emission area on the samples with and without truncated (0001) plane region, devices with three different mesa areas (50 × 50, 100 × 100, and 100 × 200 μm2) were fabricated. An increased EL intensity with the reduced mesa areas was observed in the samples without dry etching of the (0001)-plane area, because more current can be injected into the sidewall region with higher crystalline quality and luminous efficiency than the (0001)-plane MQS. Under the same injection current density, the truncated samples’ light output was increased for more than ten times as compared to the samples without (0001)-plane etching. Therefore, it confirms the possibility of realizing highly efficient GaInN/GaN MQS NWs LEDs by eliminating the (0001) plane MQS region. A precise etching and surface passivation of the apex region is expected to further reduce the reverse leakage current and improve the performance in NW-LEDs.