The thermal annealing effects on the size and composition of indium-aggregated clusters in two InGaN thin films with photoluminescence (PL) in the yellow and red ranges were studied. Various methods for investigating these effects include optical measurement, nanoscale material analysis and theoretical calculation. It was shown that in one of the samples, the major part of the PL spectrum was shifted from the yellow band into the blue range upon thermal annealing. It was observed that the photon emission spectra from the deeper layers were unaffected by thermal annealing. The quantum-confinement effects of InGaN clusters based on a quantum box model were theoretically studied.