The polyoxometalate complexes of ciprofloxacin with HnXW12O40 (X=B, Si, P) were prepared from ciprofloxacin hydrochloride and HnXW12O40·nH2O (X=B, Si, P) in aqueous solution, and characterized by elemental analysis, IR spectra and TG-DTA. The IR spectrum confirmed the presence of Keggin-type anion of heteropoly acids and the characteristic functional group of ciprofloxacin after the polyoxometalate complexes are formed. The TG/DTA curves showed that their thermal decomposition was a more-steps process consisting of simultaneous processes involving also Keggin anion. The residue of decomposition is a mixture of WO3 and B2O3, SiO2 or P2O5, confirmed by X-ray diffraction and IR spectroscopy. And the possible thermal decomposition mechanisms of the complexes are proposed.