The effects of protein removal on the physicochemical properties of waxy maize flours were investigated. Protein removal caused significant reduction in the P and S contents of starches. Starch granules had a smoother surface and low protein content (<6 g/kg) compared with the flours. Both flours and starches had a typical A-type X-ray diffraction pattern, with a crystallinity range of 29.8–32.2% and 27.7–30.6%, respectively. Flours had higher swelling power and solubility, and lower light transmittance than starches. The gelatinization enthalpy and onset temperature of starches were higher compared with those of their counterpart flours. The retrogradation of flours was significantly greater compared with that of starches. Protein removal increased the peak viscosity, trough viscosity, final viscosity, and breakdown, whereas it decreased the setback and pasting temperature. Genotypic differences in those maize were related to the physicochemical characteristics of the flours and starches.