Phytoglycogen (PG) is a hyperbranched polysaccharide with promising properties for biomedical and pharmaceutical applications. Herein, we explore the size and structure of sweet corn PG nanoparticles and their aggregation in water-ethanol mixtures up to the ethanol mole fraction xEtOH = 0.364 in dilute concentrations using small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS) measurements. Between 0 ≤ xEtOH ≤ 0.129, the conformation of PG contracts gradually decreasing up to ca. 80% in hydrodynamic volume, when measured shortly after ethanol addition. For equilibrated PG dispersions, SAXS suggests a lower PG volume decrease between 19 and 67% at the corresponding xEtOH range; however, the inflection point of the DLS volume contraction coincides with the onset of reduced colloidal stability observed with SAXS. Up to xEtOH = 0.201, the water-ethanol mixtures yield labile fractal and globular aggregates, as evidenced by their partial breakup under mild ultrasonic treatment, demonstrated by the decrease in their hydrodynamic size. Between 0.235 ≤ xEtOH ≤ 0.364, PG nanoparticles form larger, more cohesive globular aggregates that are less affected by ultrasonic shear forces.