Pure wheat endosperm was fully ground in a vibratory ball mill and structural changes in wheat starch were measured to assess the effect of mechanochemical action during the grinding process. Vibratory ball milling changed the endosperm granule size to ~30 μm (D50). There was a significant increase in damaged starch content, and this was positively correlated with the grinding time. The relative crystallinity of starch decreased by 5% after milling 105 min, and the short-range order decreased. The damaged structure of amylopectin starch decreased with milling time, as detected macroscopically by the peak viscosity and final viscosity of milling samples. Overall, the in vitro digestion results showed that mechanical modification caused irregular defects inside wheat starch crystals, increased the sensitivity of wheat starch to enzymes, enhanced the hydrolysis rate three-fold, and increased the maximum starch hydrolysis by 50%. Mechanochemistry effects was used to analyze the quality changes in wheat milling.