Sulfate plays an important role in the biosphere, hydrosphere, atmosphere, and lithosphere, and its concentration might have fluctuated greatly throughout the Earth’s history, in response to perturbations in the ocean-atmosphere system. Coupling high-resolution experimental results with an inverse modeling approach, we, here, show an unprecedented dynamic in the global sulfate reservoir during the Frasnian-Famennian (F-F) mass extinction, as one of the “Big five” Phanerozoic biotic crises. Notably, our results indicate that, in a relatively short time scale (~ 200 thousand years), seawater sulfate concentration would have dropped from several mM before the Upper Kellwasser Horizon (UKH) to a few hundreds of µM or perhaps lower at the dawn and during the UKH (more than 100 times lower than the modern level), and returned to around mM range after the event. The extremely low oceanic sulfate concentrations during the UKH would have enhanced the biological production of methane, leading to an increase in the methane efflux from the ocean and a warmer climate. Taken together, our findings indicate that the instability in the global sulfate reservoir may have played a major role in driving the Phanerozoic biological crises.