Nanoassemblies of an organic semiconductor based on thienoisoindigo were prepared by forming nanomorphologies in phase-separated films of a thienoisoindigo-based molecule (TIIG-Bz), bromobenzaldehydes (BBAs), and a phospholipid, 1,2-dioctanoyl-sn-glycero-3-phosphocholine (D8PC), and then shattering the films via penetration of water into polar domains. It was suggested that 2-BBA associated with TIIG-Bz via intermolecular halogen and chalcogen bonding between the electron-deficient δ-holes of bromine in 2-BBA and sulfur in TIIG-Bz, and their electron-rich counterparts, carbonyl oxygen, in TIIG-Bz and 2-BBA, filling empty space in the conjugated planes. This resulted in the π-π stacking of conjugated planes overwhelming the lateral packing of alkyl chains as the ratios of 2-BBA and the lipid to TIIG-Bz increased and decreased, respectively, as proven by bathochromic shifts in the absorption spectra and grazing incidence X-ray diffraction patterns. It was concluded that, by varying the 2-BBA and D8PC compositions, the water-dispersed nanomorphologies of the organic semiconductor can be controlled via the competition of hydrophobic interactions between alkyl chains for lateral association for zero-dimensional growth and intermolecular π-π interactions for one-dimensional growth.