To investigate the effect of starch granule-associated surface and channel proteins (GSCP) on starch during annealing, normal maize starch (NMS) and waxy maize starch (WMS) were subjected to protease treatment then annealing for 0–36 h to study changes in structural and physicochemical properties. The removal of GSCP accelerated the rate of increase in granule size of NMS during annealing. XRD results showed that annealing initially decreases the crystalline order of starch granules, but with prolonged annealing, the relative crystallinity increases. Also, GSCP removal decreases the rate of reduction in relative crystallinity during annealing. The lamellar structure of starch becomes compact in the initial state of annealing. With extended annealing time, the rearrangement of the microcrystalline structure may result in a decrease in compactness. The dual treatment increased the thickness of crystalline lamellae (dc), and the removal of GSCP advanced the change of lamellar structure during annealing. From pasting results, the rigidity of swollen starch was reduced after GSCP removal, while it increased with annealing time for NMS. This study adopted a GSCP removal method that had minimal impact on the structure of starch granules, providing novel information about the role of GSCP in the annealing of maize starch.