Glycogen-like glucan (GnG) is a unique hyperbranched polysaccharide nanoparticle which is drawing increasing attention due to its biodegradability and abundant short branches that can be functionalized. Because starch and GnG are both composed of glucose residues and have similar glucosidic bonds, GnG could be fabricated by sucrose phosphorylase, α-glucan phosphorylase, and branching enzymes from starch primers and sucrose. In this study, high-amylose starch, normal starch, and waxy corn starch were used as primers to synthesize GnG, and their impact on the fine structure of GnG was investigated. Structural analysis indicated that with increasing content of amylopectin in the starch primer, the proportion of short chains in GnG decreased, and the degree of β-amylolysis and α-amylolysis was enhanced. Amylose in the primer contributed to a compact and homogeneous structure of GnG, while amylopectin triggered the formation of branch points with a more open distribution. These findings provide a new strategy for regulating the fine structure of GnG.