Two perylene bisimide derivates, N,N-bi(N,N-dimethylethanamino)-1,6,7,12-tetra(4-tert-butylphenoxy)-perylene-3,4,9,10-tetracarboxylic diimide (MDI-PBI) and N,N-bi[3-(dimethylamino)-1-propyl]-1,6,7,12-tetra(4-tert-butylphenoxy)-perylene-3,4,9,10-tetracarboxylic diimide (MPI-PBI) were synthesized from perylene anhydride and tertiary amines with different alkyl chain lengths, and then self assembled in different two-phase solvent systems by rapid solution dispersion. To investigate the influences of molecular structure and assembly environment on the self-assembly of MDI-PBI and MPI-PBI, the morphology, photophysical properties and internal molecular arrangement of aggregates were characterized by SEM, UV-Vis, POM and XRD. The results showed that the solubility (S) of these two molecules in methanol was larger than that in n-hexane, and S(MPI-PBI)