Heavy metals, one of the most toxic classes of pollutants, are resistant to degradation and harmful to the biological environment. The lakes that have developed on the Tibetan Plateau are ideal regions to investigate historic heavy metal pollution, particularly through the use of the reliable 210Pb dating technique. Environmental magnetism has been successfully applied to estimate heavy metal pollution in different environmental systems due to its characteristics of simple processing steps, good sensitivity, and non-destructibility. However, it has not yet been applied to assess heavy metal pollution in lake sediments on the Tibetan Plateau. A series of environmental magnetic investigations of Qiangyong Co Lake sediments (southern Tibetan Plateau) was therefore conducted to explore the relationship between magnetic minerals and mercury (Hg) concentrations. The results showed that the magnetic mineral species in lake sediments remained stable, with similar levels of four different components from 1899 to 2011. However, the proportion of component 1 (C1, hematite) increased continuously with the corresponding decrease in the proportion of C2 (goethite), while the proportions of C3 and C4 (magnetite) did not change significantly. As a result, the bulk magnetic signals (e.g., SIRM and χlf) were unsuitable for the evaluation of the Hg concentration; however, the proportion of hematite had a strong positive correlation with the Hg concentration. It is possible that the Qiangyong Glacier (the main water supply for Qiangyong Co Lake) has experienced faster melting with global and local warming, and the Hg trapped in cryoconite and ice was released. Hematite, with a large specific surface area, has a strong capacity for absorbing Hg, and both materials are ultimately transported to Qiangyong Co Lake. The proportion of hematite in a sample is therefore a suitable semi-quantitative proxy that can be used to evaluate the Hg concentration in Qiangyong Co Lake sediments. This study confirmed that the variation of magnetic minerals can provide a new method to estimate the variation of Hg concentrations and to study the process of Hg deposition in lakes in the southern Tibetan Plateau on the basis of a detailed environmental magnetic analysis.