On the basis of our previous communication concerning a new family of thiophene-armed tetraazaanthracene molecules, we present a further intensive investigation on this class of compounds substituted with different alkyl chains and their self-assembled two-dimensional (2D) nanostructures. These tetraazaanthracene molecules with different alkyl chains were prepared in good yields using the synthetic strategy we developed. In addition to the expected typical n-type character, one compound exhibited aggregation behavior upon electrochemical reduction. Moreover, all molecules in the neutral state showed a strong tendency to aggregate in a binary solvent, as confirmed by optical spectral measurements. To investigate such self-assembly behavior, a phase-transfer method with a dichloromethane/methanol (2:3) binary solvent system was used to prepare the nanostructures. By means of atomic force microscopy, transmission electron microscopy, and X-ray diffraction, we found that the morphology of assembled 2D sheet-like structures could be adjusted by varying the alkyl chain. The weak interactions arising from the heteroatoms (N and S) in the conjugated backbones play a key role in the formation and stabilization of layered structures.