Controllable size, shape and morphology of rhodamine B/molybdic acid (RBMA) aggregates were prepared from a self-aggregation reaction in a molybdic acid and rhodamine B (RhB) coexisting solution. Nanodisks, as well as microcrystal rods and polyhexagonal microcrystal rods, have been obtained in conventional bulk solutions at different temperatures. Large-sized network microcrystal rods and branched fractal aggregates constructed with nanosubunits after the nucleation duration of an ice-water-cooled process have also been achieved under the evaporation-enhanced conditions on glass substrates. The factors affecting the size, shape and morphology of RBMA aggregates including temperature, nucleation and growth, and processing conditions are discussed. The results show that photofunctional molecules (RhB) modified the surface of the molybdic acid particles and influenced their self-aggregation. The temperature and nucleation play key roles in the formation of RBMA aggregates. The structures of RBMA aggregates were characterized by X-ray diffraction, infrared spectra and elemental dispersive spectroscopy. The results indicate that the aggregates show the characteristics of RhB-mediated hydrated ammonium molybdenum bronze with the metastable hexagonal phase. Visible-light-induced electrons transfer reactions in the RBMA aggregates from rhodamine B molecules to MoO3 matrixes were measured by UV-vis spectra and X-ray photoelectron spectra, and the fluorescent image was observed by laser scanning confocal microscopy.