Very thin metallic films deposited on a substrate often dewet upon thermal exposure, forming discrete islands of micrometer and nanometer-sized metal particles. Herein, Cu islands on Si substrate, which were formed due to agglomeration (or ‘dewetting’) of Cu thin film at 600 °C, were exposed to thermal cycling, and the ensuing evolution in their morphology was monitored. Thermal cycling was performed between either −25 °C and 150 °C or 25 °C and 400 °C, using different heating and cooling rates. With faster heating-cooling rates, a change in the shape and size of the Cu islands was observed, whereas a slow heating-cooling rate did not induce noticeable effect on their morphology. Furthermore, the formation of new nano- and micro-sized particles, probably through the dewetting of the ultra-thin layer of Cu that was left intact during the initial agglomeration treatment, was observed during the thermal cycling performed at fast rates up to 400 °C. Finite element analysis, incorporating Anand’s viscoplasticity model, revealed the existence of high strain energy density in the vicinity of the particle-Si interface when the thermal cycling is carried at a faster ramp rate, suggesting the pivotal role of thermal stresses, in addition to the maximum temperature, in controlling the morphology of the Cu particles and the dewetting of the residual ultra-thin layer of Cu on Si.