Upwelling plays a pivotal role in supplying methylmercury (MeHg) to the upper oceans, contributing to the bioaccumulation of MeHg in the marine food web. However, the influence of the upwelling of Circumpolar Deep Water (CDW), the most voluminous water mass in the Southern Ocean, on the MeHg cycle in the surrounding oceans and marine biota of Antarctica remains unclear. Here, we study the mercury (Hg) isotopes in an ornithogenic sedimentary profile strongly influenced by penguin activity on Ross Island, Antarctica. Results indicate that penguin guano is the primary source of Hg in the sediments, and the mass-independent isotope fractionation of Hg (represented by Δ199Hg) can provide insights on the source of marine MeHg accumulated by penguin. The Δ199Hg in the sediments shows a significant decrease at ∼1550 CE, which is primarily attributed to the enhanced upwelling of CDW that brought more MeHg with lower Δ199Hg from the deeper seawater to the upper ocean. We estimate that the contribution of MeHg from the deeper seawater may reach more than 38% in order to explain the decline in Δ199Hg at ∼1550 CE. Moreover, we found that the intensified upwelling may have increased the MeHg exposure for marine organisms, highlighting the importance of CDW upwelling on the MeHg cycle in Antarctic coastal ecosystems.