Starch is the main substrate in millet thick wine (MTW). In order to control the fermentation process of MTW, it is critical to monitor changes in the starch structure and physicochemical characteristics during the fermentation of MTW. In the present study, the structural characteristics of MTW starch were analyzed by scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and rapid viscosity analysis (RVA). The results of SEM and CLSM showed that large starch granules in MTW swelled, developed cavities, and ruptured or even vanished with the prolongation of the fermentation time, whereas the size and shape of small starch granules barely changed, only falling off the pomegranate-seed-like aggregates. With the increase in fermentation time, the relative crystallinity of starch in MTW gradually increased. In addition, the short-range ordered structures underwent complex changes. Changes in the starch morphology and ordered structure led to an increase in the peak viscosity time and the initial gelatinization temperature. The present results reveal the beneficial effect of fermentation on MTW processing and suggest its potential applications in other millet-based fermented products.