Using the Yumai 49-198 variety, wheat starch was prepared by the dough-washing method, and A- and B-type wheat starches were separated by sedimentation. Subsequently, A- and B-type starch were defatted and deproteinized. The effect of lipids and particle-bound proteins on physiochemical and structural properties of A- and B-type wheat starch were studied in terms of changes in starch composition, particle structure, solubility, swelling power, pasting properties, and thermal properties before and after treatment. The results indicated that compared with untreated wheat starches, the particles of defatted and deproteinized wheat starches were smoother and had more uniform dispersion. The position and shape of birefringence were not significantly changed, but the clarity was markedly higher. The solubility and swelling degree was dramatically increased with increasing temperature. The onset temperature, peak temperature, final temperature, transparency, peak viscosity, breakdown value, and setback value were also significantly increased. However, the freeze-thaw stability and peak-time value were markedly decreased, and no significant changes were observed in gelatinization enthalpy. These results may have theoretical reference for industrial use of A- and B-type wheat starches.