<p>Seawater Mg/Ca has oscillated markedly over the Phanerozoic, closely associated with secular variations in sedimentation, icehouse-greenhouse fluctuations, and the evolution of calcifying invertebrates. However, the drivers of these long-term oscillations remain unresolved. Here, we develop an inverse model that couples seawater Mg concentration and Mg isotope composition variations. By exploiting the contrasting Mg isotopic fractionation associated with Mg-silicate formation and dolomitization, this model quantifies the major marine Mg sinks. Model results show that increases in seawater Mg/Ca during supercontinent assembly were explained by reduced rates of silicate alteration and dolomitization. In contrast, decreases in seawater Mg/Ca during periods of supercontinent stasis and early breakup were driven by intensified Mg-silicate formation and dolomitization. Variations in marine Mg-silicate and dolomite formation were further regulated by seafloor spreading, continental configuration, and climate throughout the supercontinent cycle. Together, our results identify the supercontinent cycle as a first-order regulator of Phanerozoic seawater Mg/Ca through its control on marine Mg-silicate and dolomite fluxes.</p>