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Rationale: The research area of ion clusters has helped to enrich the study of chemical bonding theory, clarify the crystal nucleation process and investigate the cluster ion–molecule reactions. The mass spectrometry (MS) technique, especially high‐resolution MS, is an important method for investigating ion clusters in the gas phase. As polyoxometalates (POMs) have been attracting considerable interest in biochemistry, medicine and materials science due to their excellent structural and electronic features it is important to characterize these clusters by MS. Methods: Singly negatively charged molybdenum‐containing and tungsten‐containing ion clusters with different matrices were produced by Keggin‐type silicopolyoxometalate anions under matrix‐assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI‐FTICR MS) conditions. Results: The matrices displayed an obvious influence on the formation of ion clusters. It was found that the molybdenum‐containing ion species [(HSiO3)(MoO3)n]−, [(SiO2)m(MoO3)n(H2O)x] −•, [(OH)(MoO3)n]−•, [(MoO3)n]‐•, and [HxSiMoyOz]− were the main ion series in the mass spectra. For the tungsten‐containing ion clusters, [(HSiO3)(WO3)n]−, [(C8H5Om)(WO3)n(H2O)x]−, [(OH)(WO3)n]−, and [(WO3)n]‐• were the main ion species in the mass spectra, and a series of organic–inorganic hybrid tungsten‐containing ion clusters [(C8H5Om)(WO3)n(H2O)x]− were generated by the interaction of DHAP and THAP matrices with tungstate anions. Furthermore, the most abundant species (magic number) in each ion series indicated that they might adopt more stable structures than other relevant clusters. Conclusions: Keggin‐type silicopolyoxometalate anions can produce several series of singly charged molybdenum‐containing/tungsten‐containing ion clusters in negative‐ion generating mode under MALDI conditions. It is proposed that the "Lucky Survivors" hypothesis may be used to illustrate the generation of ion clusters in the gas phase during the early stages of plume expansion. In addition, clear evidence of hydrogen transfer and electron capture to POMs was found in the obtained MALDI mass spectra. These results highlight the utility of the MALDI‐FT method for obtaining novel ion clusters and also show the stability of these clusters. [ABSTRACT FROM AUTHOR]