Freeze-drying (FD) and cryo-milling (CM) are common methods for preparing powder gelatinized starch samples. This study investigates the structural characterization of raw/gelatinized maize starches and digestibility after FD/CM processes to elucidate their effect on starch digestibility determination. Results showed that FD slightly increased digestibility, while higher initial glucose content in CM samples, especially for gelatinized samples. Only FD retained the granular morphology and relative crystallinity (RC), while gelatinized-FD decreased RC by 75%. CM decreased RC by 12%, while gelatinized-CM decreased it by 97%. Combined with short-range and chain structural results, FD tended to disrupt internal connected chains through volume stress, while CM cleaved glycosidic bonds in external chain. Stretched chains in gelatinized starch promoted the breakage of chains during shearing and their efficient binding with digestive enzymes. These findings would provide a basis for pre-treatment of powder samples and processes of starch- rich foods. Display omitted •Cryo-milling (CM) increased gelatinized starch digestibility than freeze-drying (FD).•The volume stress of ice crystal formation-sublimation acts on connected chains.•Shear degradation effect of CM caused cleavage of α-1, 6- and 1, 4-glycosidic bonds.•Stretched chain structure rose the susceptibility of starch to followed CM and FD.•It merits pre-treatment of gelatinized starch and development of starchy foods.