Four polyoxometalate complexes, (CPFX·HCl)3H4SiW12O40, (CPFX·HCl)3H3PW12O40, (CPFX·HCl)3H3PMo12O40 and (CPFX·HCl)4H4SiMo12O40, were prepared from ciprofloxacin hydrochloride(CPFX·HCl) reacting with HnXM12O40·nH2O(X=P,Si; M=W,Mo) in an aqueous solution, and characterized by elemental analysis, IR spectrometry and TG-DTA. The IR spectrum confirms the presence of Keggin-type anions of heteropoly acids and the characteristic functional groups of ciprofloxacin. The TG/DTA curves show that their thermal decomposition is a multi-step process including simultaneous collapse of the Keggin-type structure. At first, these compounds had a mass loss of water molecules, then several other mass losses occurred due to the decomposition of ciprofloxacin hydrochloride and its fragments with the degradation of Keggin anions. The end product of decomposition is the mixture of WO3(or MoO3) and SiO2(or P2O5), identified by X-ray diffraction and IR spectroscopy. The possible thermal decomposition mechanisms of these complexes are proposed. This study exemplified that the thermal stability of the complexes containing tungsten is much better than that of the complexes containing molybdenum.