Molecular self-assembly of aromatic organic molecules based of imidazo[1,2-a]pyridine ring system has been successfully accomplished by regiospecific modulation of substituents such as electron withdrawing (formyl and nitro) and electron releasing (methyl) groups. Interestingly, even a slight structural variation of functional group at specific position(s) resulted in diverse micro/nano-scaled self-assembled morphologies such as needles, fibrils, dendrites, plates and A-shaped structures which were characterized using optical microscopy, confocal microscopy, SEM and AFM. Further, TGA and XRD studies were carried out to determine the stability and self-assembling interactions, respectively. The computational studies were performed to explore the effect of substituents on π-electron density of the electron cloud over the ring which directly correlated ring electron density with electronic substituents. Notably, the present study postulates a novel hypothesis based on experimental evidences that the modulation of π-electron density by functional group variation in heteroaryl systems can lead to fabrication of a variety of self-assembled structures.