The role of pi-pi stacking in the molecular self-assembly behaviour, the phase transitions and fluorescent properties was investigated for coil-rod-coil liquid crystals with two ethylene oxide coil units and aromatic azomethine rod units. Three kinds of rod-coil liquid crystals with different rod units were synthesized and characterized by differential scanning calorimetry (DSC), polarized optical microscope (POM), X-ray diffraction (XRD), transmission electronic microscope (TEM), absorption and photoluminescence. With strong pi-pi stacking interaction between coplanar compounds, fibril structure in solution is formed while the fluorescent emission shows a quick increase of the intensity of short wavelength with the increase of solution concentration. Spherical aggregations in solution are formed with the increase of the twisting of the rod segment plane, which decreases the pi-pi stacking interaction and thus enlarges the intermolecular spacing. Simulation work carried out in Material Studio corresponds well with the experiment results of aggregations and phase transitions.