α-MoO3 microspheres assembled by nanorods were synthesized in room temperature ionic liquids (bmimBF4: 1-butyl-3-methylimidazolium tetrafluoroborate) by microwaves heating method. The microstructure and morphology of the products were characterized by the techniques of X-ray powder diffraction (XRD), Fourier-transform spectrometer (FTIR), scanning electron microscope (SEM), transmission electron microscope (TEM). The influence factor such as the amount of ammonium heptamolybdenum tetrahydrate in ionic liquids was investigated in detail. The possible reaction mechanism was also discussed. It was demonstrated that the ionic liquid could act as template agent for the formation of α-MoO3 microspheres. The present synthesis route is very simple and fast, and could be extended to the fabrication of other nanomaterials in ionic liquids.