Volcanic eruptions are thought to be a key driver of rapid climate perturbations over geological time, such as global cooling, global warming, and changes in ocean chemistry. However, identification of stratospheric volcanic eruptions in the geological record and their causal link to the mass extinction events during the past 540 million years remains challenging. Here we report unexpected, large mass-independent sulphur isotopic compositions of pyrite with Δ33S of up to 0.91‰ in Late Ordovician sedimentary rocks from South China. The magnitude of the Δ33S is similar to that discovered in ice core sulphate originating from stratospheric volcanism. The coincidence between the large Δ33S and the first pulse of the Late Ordovician mass extinction about 445 million years ago suggests that stratospheric volcanic eruptions may have contributed to synergetic environmental deteriorations such as prolonged climatic perturbations and oceanic anoxia, related to the mass extinction.