The experimental synthesis shows that the substituent of alkyl side chain can significantly change crystal structures of DPND. For instance, the DPND6 and DPND aggregates have different transverse and longitudinal shifts and intermolecular distances. Those structure differences result in quite different mixing components of FE and CT states in the adiabatic excited states, subsequently produce the different absorption spectral characters. However, it is nontrivial to reveal the structure-property relationship in organic aggregates because of complex dynamic processes from many-body interactions, such as the long-range excitation energy transfer, electron and hole transfer and molecular vibrational motions, etc.