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Current research on maize germination suffers from long sampling intervals, and the relationship between the starch structure and the processing properties of flour in maize is still unclear. This study observed the effect of germination on the structure and composition of maize starch and the processing properties of maize flour over a 72 h period using a short interval sampling method. At 36 h, the short-range ordered structure, crystallinity, and enthalpy of starch reached the highest values of 1.02, 34.30%, and 9.90 J/g, respectively. At 72 h, the ratios of rapidly-digested starch (RDS) and slowly-digested starch (SDS) enhanced to 29.37% and 28.97%; the RS content reduced to 35.37%; and the flow properties of the starch were improved. This study enhances the understanding of the effects of germination on the processing properties of maize starch and flour, determines the appropriate application, and recommends the use of germination in the food industry.