As the most promising optoelectronic device in the 21st century, the research of epitaxial structure of light-emitting diode has been a hot topic for scientists.Three types of InGaN/GaN micro-array with different morphologies were grown on graphical sapphire substrate by selective regional epitaxy using metal organic chemical vapor deposition technology. The size of the array is 6 μm. The tablets array is dominated by (0001)c facet, the height is 0.6 μm; the platelets array includes one (0001)c facet and six equivalent (10-11) semi-polar facets, the height is 1.2 μm; the pyramid-like array is dominated by (10-11) semi-polar facet and the height is 5 μm. The luminescence properties of InGaN/GaN micro-array structure were characterized by micro-area photoluminescence spectrometer and the results show that InGaN/GaN micro-array with different morphologies could achieve multi-wavelength emission, but its luminescence properties are heavily dependent on the morphology. Cathodic fluorescence spectra results show that the InGaN/GaN platelets array’s wavelength covering red, green and blue was obviously different for different test positions, which is mainly attributed to surface migration effect and transverse gas phase diffusion resulting in nonuniform distribution of In content in each position. Moreover, the results of energy dispersive spectrometer analysis show that the In content on different facets are different, and the (0001)c facet content is more than that of (10-11) semi-polar facets. For the realization of multi-emission and new optoelectronic device design, the successful preparation InGaN/GaN micro-array is very significance.