Changes in the content and morphology of residual starch in Zaopei during strong-flavor Baijiu fermentation are investigated. The results show that the residual starch content increases through the Baijiu production and that the residual starch content of distiller's grains (DGS) is the highest (76.35%). The crystalline structure of starch changes from A-type (raw grain starch) to B + V-type (Zaopei, Hongzao, Mianzao, DGS). The upper Zaopei starch has the typical diffraction peaks of B + V-type (7.4°, 12.8°, 14.9°, 19.7°, 19.6°, 26.6°) and retains the typical diffraction peaks of A-type (17.0°, 22.2°). The intermediate and bottom Zaopei starch has the typical diffraction peaks of B + V-type (7.4°, 12.8°, 16.9°, 19.7°, 20.7°, 26.6°) and loses the typical diffraction peaks of A-type. With the progression of Baijiu production, the gelatinization temperature and enthalpy of starch increase, while the water-holding capacity, freeze-thaw stability, solubility, and swelling power decrease. The above results show that the starch complex is the primary form of residual starch in strong-flavor Baijiu.