• Trace metal contamination in soils of 29 China’s mountains was investigated.
• Cd was the priority control metal with moderate to heavy contamination.
• Cd and Pb contamination were higher in northwest, south and southwest China.
• Atmospheric deposition was the main sources of Cd and Pb in soils.
• Climate, vegetation and soil properties regulated spatial distribution of trace metals.
Trace metal contamination in soils is a threat with an uncertain limit to maintain planet safety, and the issue of trace metal contamination in mountain soils is still of low concerned. In this study, we assessed the contamination of six trace metals (Cd, Cr, Cu, Ni, Pb, and Zn) in mountain soils across China and deciphered the potential drivers of their spatial distribution. The results showed that concentrations of Cd and Pb decreased significantly with soil depth, and their concentrations were markedly higher in north-west, south, and south-west China than elsewhere. Among the metals, Cd was the priority for control with moderate to heavy contamination, followed by Pb, whereas the other metals did not show evident contamination. The altitudinal pattern and isotopic tracing revealed that the significant enrichment and marked contamination of Cd and Pb in surface soils were primarily attributed to deposition through long-range transboundary atmospheric transport and condensation. Ore mining, nonferrous smelting, and coal and fuel combustion were identified as primary anthropogenic sources of the Cd and Pb. Soil organic matter content, pH, and soil forming processes directly determined the accumulation of trace metals in the soils, and orographic effects, including local climate, vegetation composition, and canopy filtering, regulated the spatial distribution of the metals. This study highlights the significance of soil Cd contamination in mountains, which are considered of low concern, and suggests that long-term monitoring of trace metal contamination is necessary to improve biogeochemical models that evaluate the responses of the mountain critical zone to future human- and climate-induced environmental changes.