The pi-stacking structures and self-association thermodynamics of N, N'-di(n-alkyl) quinacridone derivatives (n-alkyl QAs) with various substituents on the side aromatic rings and different length of n-alkyl chains are investigated in organic solvents by (1)H NMR spectroscopy. The stacking geometries are built based on both the magnitudes and directions of peak shifts with concentration and solvent polarity. The intermolecular interaction between nitrogen atoms and oxygen atoms dominates the general geometrical preferences of the stacking in which the molecules are face-to-face arranged in a parallel and an antiparallel fashion, respectively. The stacking structures are little affected by the length of the n-alkyl chains but are regulated in an allowed range by the size and properties of the substituents. The association processes of all the n-alkyl QAs are enthalpically favorable at 298 K, while the relative stability of these n-alkyl QAs assemblies is governed mainly by the entropy of the association processes. The introduction of larger substituents and longer n-alkyl chains disfavors the association of the n-alkyl QAs, while the binding of the halogen atoms on the side aromatic rings is favorable to the association. The relative strength of the stacking interaction for the substituted n-alkyl QAs has not obvious correlation with the electron-donating or electron-withdrawing nature of the substituents, while it is well associated to the dispersion energy and repulsive exchange energy. The different entropy-enthalpy compensation of the halogen-substituted n-alkyl QAs from others may suggest different association mechanism for the two types of n-alkyl QAs.