In this study, we applied capillary zone electrophoresis (CZE) to investigate the solution stability and equilibria of pentamolybdobis(phenylphosphonate), [(C6H5PO3)2Mo5O15]4–, which is a Strandberg‐type of polyoxometalate (POM) with considerable promise as an antiviral and anti‐HIV chemotherapeutic agent. This is achieved by analyzing the intensities and shapes of the three peaks in the CZE electropherogram that correspond to the three components involved in the equilibria, that is, [(C6H5PO3)2Mo5O15]4–, [Mo7O24]6–, and [Mo8O26]4– anions. The dependence of the equilibria of pentamolybdobis(phenylphosphonate) on various conditions, including sample concentration, counterion, and solution pH, was investigated through CZE. The interactions of pentamolybdobis(phenylphosphonate) with amino acids and cyclodextrins in solution were also investigated and discussed on the basis of the CZE results. Our study indicates that CZE has great potential as a simple, low‐cost, and efficient method to monitor the synthesis, purity, stability, and solution equilibria of POMs.