In this study the effects of the annealing temperature on the InGaN/GaN solar cells with different In-contents grown on sapphire substrate by the Metal Organic Chemical Vapor Deposition (MOCVD) are analyzed by High Resolution X-ray Diffraction (HRXRD) and an Atomic Force Microscope (AFM). The plane angles, mosaic crystal sizes, mixed stress, dislocation intensities of the structure of the GaN and InGaN layers are determined. According to the test results, there are no general characteristic trends observed due to temperature at both structures. There are fluctuating failures determined at both structures as of 350 °C. The defect density increased on the GaN layer starting from 350 °C and reaching above 400 °C. A similar trend is observed on the InGaN layer, too.