Boring pests such as Sitophilus zeamais (S. zeamais) are major threats in grain storage. However, how these pests affect the proteins of stored grains remains largely unknown. Here we aimed to investigate the effect of S. zeamais infestation on wheat protein during postharvest storage. In this study, wheat grain infested by S. zeamais was sampled at egg (4 d), larval (20 d), pupal (35 d), and adult stages (45 d), respectively. The protein's physicochemical and structural properties and the edible quality of whole wheat noodle were analyzed. The results showed that S. zeamais infestation significantly decreased the quality of wheat protein by altering its constitution and structure properties. Especially, compared with the control, the content of wet and dry gluten, gluten index, sodium dodecyl sulfate sedimentation volume, sulfhydryl groups, and disulfide bonds in insect-infested wheat decreased by 19.40, 5.42, 18.40, 8.12, 29.13, and 14.30%, respectively, during the storage period of one life cycle of S. zeamais. Additionally, the proportions of wheat protein fractions (albumin [1.16-fold], globulin [0.96-fold], gliadin [1.16-fold], and glutenin [0.95-fold]) and secondary structures (α-helix [0.91-fold], β-fold [0.96-fold], β-turn [1.06-fold], and random coil [1.05-fold]) of protein changed significantly, and the gluten network structure was broken in S. zeamais-infested wheat. Furthermore, the color of whole wheat noodle became darker, cooking loss rate increased, and textural properties (hardness, adhesiveness, springiness, cohesiveness, chewiness, and resilience) decreased as well. The results in the present study provided new insights for analyzing the quality deterioration mechanism and further quality improvement of boring pests-infested wheat grain.