To determine the rapidly digestible starch (RDS), slowly digestible starch (SDS), and resistant starch (RS) contents in a starch sample, the addition of amyloglucosidase is often used to convert hydrolyzates from α-amylase digestion to glucose. The objectives of this study were to investigate the exact role of amyloglucosidase in determining the digestibility of starch and to understand the mechanism of enzymatic actions on starch granules. Four maize starches differing in amylose content were examined: waxy maize (0.5% amylose), normal maize (≈27% amylose), and two high-amylose starches (≈57 and ≈71% amylose). Notably, without amyloglucosidase addition, the RS content increased from 4.3 to 74.3% for waxy maize starch, 29.7 to 76.5% for normal maize starch, 65.8 to 88.0% for starch with 57% amylose, and 68.2 to 90.4% for the starch with 71% amylose. In the method without α-amylase addition, less RS was produced than without added amyloglucosidase, except in maize at 71% amylose content. Scanning electron microscopy (SEM) revealed the digestive patterns of pinholes with α-amylase and burrowing with amyloglucosidase as well as the degree of digestion between samples. To understand the roles of amyloglucosidase and α-amylase in the in vitro test, multiple analytical techniques including gel permeation chromatography, SEM, synchrotron wide-angle X-ray diffraction, and small-angle X-ray scattering were used to determine the molecular and crystalline structure before and after digestion. Amyloglucosidase has a significant impact on the SDS and RS contents of granular maize starches.