Heteropoly compounds are of great practical importance as components of catalysts. In particular, phosphomolybdic acid H3PMo12O40 is widely used in catalytic oxidation processes. For heterogeneous catalysts, one of the effective methods for studying their structure is mass spectrometry. In this work, the main patterns of fragmentation of crystalline phosphomolybdic acid and its aqueous solutions are studied by laser desorption/ionization. It has been found that during laser desorption/ionization, acid crystals tend to form particles of the cluster type (MoO3)n and HPO3∙(MoO3)n. When registering positive ions, particles with a mixed oxidation state of Mo+ 5 and Mo+ 6 were detected. Clusters of molybdenum (VI) oxide were found in the study of aqueous solutions of acid. In the study of aqueous solutions together with a matrix of 2,5-dihydroxybenzoic acid, particles containing a hydrated molecular ion were found. Clusters with a molecular ion were identified: H3PMo12O40∙(MoO3)3, H3PMo12O40∙(MoO3)4, H3PMo12O40∙MoO3∙4H2O, H3PMo12O40∙(MoO3)2∙2H2O, H3PMo12O40∙(MoO3)2∙4H2O, and H3PMo12O40∙(MoO3)3∙2H2O. When studying the influence of the LDI parameters on the informativity of the mass spectrum, it was found that, in the general case, the values of the peak intensity and the laser power, as well as the number of shots, are in symbatic dependence. The intensity of the peak depends largely on the power of the laser than on the number of shots. Thus, it has been shown that, upon ionization, phosphomolybdic acid can generate both fragments and cluster ions containing mainly the adduct of the molecular ion with molybdenum oxide and water.