Moss is usually as an initial colonizer in alpine glacier retreated regions. We hypothesized that moss can significantly facilitate the toxic metals accumulation in alpine ecosystems based on its strong ability of absorption and the role in soil development. Hence, we investigated the trace element pool sizes and enrichment factors, especially for mercury (Hg) by using the Hg isotopic compositions to determine the source contributions in a moss-dominated ecosystem over glacial erratic in Eastern Tibetan Plateau. Results show that Hg, lead (Pb) and cadmium (Cd) are highly enriched in organic soils. Specifically, Cd concentration is 5–20 times higher than the safety limit of the acid soil (pH ≤ 5.5) in China. Atmospheric depositions dominantly contribute to the Pb and Cd sources in organic soils, and followed by the moraine particles influences. The lowering pH in organic soils increasing with glacial retreated time results in the desorption of Cd in organic soils. Atmospheric Hg⁰ uptake by moss predominantly contributes to the Hg sources in organic soils. The average Pb accumulation rate over last 125-year is about 5.6 ± 1.0 mg m⁻² yr⁻¹, and for Cd is 0.4 ± 0.1 mg m⁻² yr⁻¹, and for Hg⁰ is 27.6 ± 3.2 μg m⁻² yr⁻¹. These elevated accumulation rates are caused by the high moss biomass and elevated atmospheric Hg, Pb and Cd pollution levels in China and neighbouring regions. Our study indicates that the moss not only as the bioindicator, but also plays an important role in the hazardous metal biogeochemical cycling in alpine regions.