The structure and properties of phytoglycogen and glycogen subjected to acid hydrolysis was investigated using amylopectin as a reference. The degradation took place in two stages and the degree of hydrolysis was in the following order: amylopectin > phytoglycogen > glycogen. Upon acid hydrolysis, the molar mass distribution of phytoglycogen or glycogen gradually shifted to the smaller and broadening distribution region, whereas the distribution of amyopectin changed from bimodal to monomodal shape. The kinetic rate constant for depolymerization of phytoglycogen, amylopectin, and glycogen were 3.45 × 10−5/s, 6.13 × 10−5/s, and 0.96 × 10−5/s, respectively. The acid-treated sample had the smaller particle radius, lower percentage of α-1,6 linkage as well as higher rapidly digestible starch fractions. The depolymerization models were built to interpret the structural differences of glucose polymer during acid treatment, which would provide guideline to improve the structure understanding and precise application of branched glucan with desired properties.