Coastal sediments are a major sink of the global mercury (Hg) biogeochemical cycle, bridging terrestrial Hg migration to the open ocean. It is thus of substantial interest to quantify the Hg contributors to coastal sediments and the extents to which the Hg sequestered into coastal sediments affects the ocean. Here, we measured concentrations and isotope compositions of Hg in Chinese coastal sediments and found that estuary sediments had distinctly higher δ202Hg and lower Δ199Hg values than marine sediments. Hg isotope compositions of marine sediments followed a latitudinal trend where δ202Hg decreases and Δ199Hg increases from north to south. An integrated model was developed based on a Hg isotope mixing model and urban distance factor (UDF), which revealed a significant difference in Hg source contributions among the estuary and marine sediments and a gradual change of dominant Hg sources from terrestrial inputs (riverine and industrial wastewater discharges) to atmospheric deposition with a decrease in urban impact. A UDF value of 306 ± 217 was established as the critical point where dominant Hg sources started to change from terrestrial inputs to atmospheric deposition. Our study helps explain the input and migration of Hg in Chinese marginal seas and provides critical insights for targeted environmental management.