The structural evolution with the self-assembly and self-alignment progress of the typical Lyotropic Chromonic Liquid Crystals (LCLCs) molecules, Sunset Yellow FCF (SSY), was studied by time-resolved grazing-incidence wide-angle X-ray scattering (GI-WAXS). It was revealed that the SSY molecules oriented by the initial shear flow gradually assembled and was oriented by solvent evaporation. Then, the drastic progress in the assembly and orientation occurred accompanying the electrostatic interaction between the assembled aggregates.