Starch is depolymerized by enzymes to produce converted products in industry. Understanding the relationship between starch structure and α-amylase hydrolysis can provide a theoretical basis for raw starch sugar production. Starch granule-associated proteins (SGAPs) are naturally located on the surface, channel and interior of starch granules, which are respectively called starch granule surface proteins (SGSPs), channel proteins (SGCPs) and intrinsic proteins (SGIPs). SGSPs and SGCPs are in directly contact with the external environment and may serve as the first barrier for external substances (e.g., enzyme molecules) to influence starch hydrolysis. To investigate the impacts of SGAPs on the α-amylase hydrolysis of starch, SGSPs and SGCPs of waxy, low-amylose and high-amylose rice starches were removed. The results showed that the hydrolysis rate coefficients (k, min-1) of WRS, LARS and HARS were 4.66×10^-3, 4.02×10^-3 and 1.22×10^-3, respectively. After the removal of SGSPs and SGCPs, the hydrolysis rates of waxy, low-amylose and high-amylose rice starches increased, which were 1.63×10^-2,7.19×10^-3 and 1.67×10^-3, respectively. At the molecular level, the proportion of short chains (fa) increased and the proportion of long chains (fb3) decreased during α-amylase hydrolysis. At the lamellar level, the thickness of amorphous lamellae (da) decreased and the thickness of crystalline lamellae (dc) increased. After the removal of SGSPs and SGCPs, earlier or more pronounced changes in semi-crystalline lamellae and amylopectin chain lengths were observed. At the granular level, the lateral and longitudinal expansion of the channels and cavities in starch before and after removing SGSPs and SGCPs occurred simultaneously during α-amylase hydrolysis, which was called the "inside-out" hydrolysis pattern. Therefore, SGSPs and SGCPs limit α-amylase accessibility via physical barriers or site occupation, without altering the hydrolysis pattern but accelerating its progression. This study will help in increasing raw starch sugar production.