Tree-shaped molecules consisting of octa-p-phenylene as a stem segment and oligoether dendrons as a flexible head were synthesized and characterized. The molecular tree based on a small flexible head self-assembles into a lamellar structure, whereas the molecule based on a larger headgroup self-assembles into a discrete heptameric bundle that organizes into a 3-D primitive orthorhombic supercrystals, as confirmed by X-ray scatterings and transmission electron microscopic (TEM) observations. Optical studies revealed that the absorption and emission maxima and absorption edge of the 3-D structure shift to higher energy compared to those of the lamellar structure. The molecules in dilute solution (THF/ water = 1:10 v/v) were observed to self-assemble into capsule-like hollow aggregates, as confirmed by dynamic and static light scatterings, scanning electron microscopy (SEM), and TEM investigations. These results demonstrate that tree-shaped molecules are capable of packing into organized discrete nanocrystals with parallel arrangement as well as hollow nanocapsules with radial arrangement, depending on the presence of selective solvents for flexible headgroup.