<p>Heavy metal contamination in the mining–agriculture ecotones is influenced by lithogenic enrichment, industrial emissions, and agricultural inputs. Currently, knowledge of the vertical patterns and risk pathways in these environments is insufficient. In this study, paired soil profiles from mining and smelting areas of the manganese triangle (Xiushan, Chongqing, China) were analyzed to assess their physicochemical properties, metal concentrations, and ecological and health risks. The pH value was higher in the smelting soils (6.4–6.8) than in the mining soils (5.9–6.1). This similar trend was also observed in As and Pb, whereas contrary trend appeared in Zn and Cu. By contrast, Mn, Fe, Cr, Co, Sb, Se, and S concentrations remained stable across profiles, which indicated they had strong lithogenic controls. Pollution indices identified Sb (single-factor pollution index: &lt; 9.15) and Cd (single-factor pollution index: 3.44–3.76) as dominant pollutants. The potential ecological risk index attributed 43.0% of the ecological risk in mining soils to Cd and 38.1% of the risk in smelting soils to Sb. Ecological risk classifications indicated moderate risks for smelting soils across depths, while mining soils exhibited greater variability with localized high-risk zones. In a human health risk assessment, the dominant contributors to carcinogenic and noncarcinogenic risks were ingestion (&gt; 95%) and dermal contact (73%–80%), respectively, and inhalation had a negligible contribution. These results show mining- and smelting-derived metals have distinct vertical geochemical behaviors, which provides a mechanistic basis for targeted risk management in mining–agriculture ecotones.</p>