Abstract: Mercury (Hg) and its methylated product, methylmercury (MeHg), are highly toxic. Sediments act as both sources and sinks for mercury in water. Their potential ecological risks can pose a serious threat to human health and the environment. This study investigated the distribution characteristics of Hg and MeHg in surface sediments of typical lake areas (algal lake area, central lake area, and macrophyte lake area) in Taihu Lake, and analyzed the influencing factors and conducted ecological risk assessment. The results show significant differences in the distribution characteristics of mercury and methylmercury in sediments from different ecological types of lake areas. The algal lake area had significantly higher concentrations of total mercury (THg) and MeHg than the central lake area and macrophyte lake area. The geoaccumulation index method indicate that THg in surface sediments of the algal lake area (Zhu Shan Bay and Gonghu Bay) reached a moderate level of pollution, while THg in surface sediments in the centre of the lake and macrophyte lake areas was at a moderate level of pollution. Correlation analysis indicate that mercury in sediments is negatively correlated with dissolved oxygen (DO), pH, and redox potential (ORP) in the water body, and positively correlated with the degree of nutrient enrichment of the water body as well as sediment C/N and organic matter. The determination of functional gene abundance show that the specific methanogenic functional gene dsrB of sulfate-reducing bacteria is the main microorganism involved in the reduction and methylation metabolism of Hg in the sediments of Taihu Lake. This study provides robust theoretical support for the environmental management and risk assessment of mercury in different ecological types of Taihu Lake.