A novel molecule-ion adduct of ammonium molybdate tetrahydrate (AMT) with beta-cyclodextrin (CD) was prepared in this work. Significant differences in spectral properties between AMT and the adduct AMT-beta-CD were observed by a series of experimental probes, such as powder X-ray diffraction, Fourier transformation infrared spectroscopy, and Raman spectroscopy. Field emission scanning electron microscopy showed that, although the crystal growth of AMT-beta-CD was dominated by the molecular stacking of AMT, the size and morphology of the adduct were rather different from those seen in free AMT. The difference in stacking forms was attributed to the contribution of the molecule-ion interaction between AMT and beta-CD. A drastic improvement in thermal stability of AMT and beta-CD after adduct formation was observed by thermogravimetry analysis, which was confirmed by controlled sintering measurements. This revealed that the adduct interaction between them played an important role in mediating the thermal decomposition process of the adducted components. Furthermore, our results indicated that AMT and its adduct had a different performance in the catalytic desulfurization of thiophene and its derivatives. The fact that the catalytic efficiency of AMT was decreased after adduct formation implied there was a complexation between AMT and beta-CD. Besides, several unusual molecular ions--NH(3)(+), NH(2)(+), and NH(+)--were simultaneously found with gas chromatography coupled to time-of-flight mass spectrometry of free AMT.