By combining the first-principles calculations for constructing the model Hamiltonian and the Non-Markovian stochastic Schrödinger equation for photo-physical simulations, we have theoretically investigated the effect of alkyl side chains on the spectral characteristics and exciton dynamics of the aggregates of DPND skeleton. The results elucidate that the substituent has minor effects on the electronic properties of single molecule, but the existing of alkyl side chains will modulate the intermolecular packing arrangement and affect the intermolecular interactions, subsequently alter the spectral characteristics and exciton dynamics processes.