The natural heavy metal contaminant is severe in the Karst area in Guangxi. In this area, the soil contains large quantities of Fe-Mn nodules. Soil Fe-Mn nodules are symbiotic products of soil formation, which is controlled by the environmental conditions. Therefore, Fe-Mn nodules is a good geological record of soil formation and development, as well as historical environmental change. Fe-Mn nodules are composed of ferromanganese oxides, which have strong capacities for heavy metal adsorption. Studying the accumulation characteristics of heavy metals in Fe-Mn nodules will improve understanding the accumulation processes of heavy metals during soil formation and provide scientific support for soil management and treatment. In this study, a series of experiments were conducted using the soil and Fe-Mn nodules from a typical Karst area in Liujiang, Guangxi. Through the determination of trace elements, the analysis shows that Fe-Mn nodules can adsorb Ni, Cu, Cd, Zn, Pb, Co, Ba, As and Cr effectively. We found concentric ring structure and regular distribution of elements in nodules by means of micro measurement methods including Raman spectrum and SEM-EDS. Combined with internal structure and elemental distribution characteristics, the formation mechanism and material source of Fe-Mn nodule was speculated. The formation of Fe-Mn nodules immobilized heavy metals and reduced heavy metal pollution in soil. However, the dissolution of Fe-Mn nodules will release large amount of heavy metals into soil especially those associated with Mn.