The ferromanganese nodules (FMNs) developing in soils of karst regions are naturally characterized by high heavy metal(loid)s contents due to several geological factors. Soil FMNs can considerably influence the geochemical behaviors of soil heavy metal(loid)s. However, the mechanisms of the FMN effects in soils of karst areas soils remain unclear, resulting in less understanding of the development process of karst soils. Therefore, the present study aims to investigate 21 individual FMNs collected in soils derived from carbonate rocks in Guangxi province, China, to reveal the mechanisms of heavy metal(loid)s enrichment in FMNs. The studied soil FMNs were mainly composed of Fe2O3, SiO2, Al2O3, MnO2, and TiO2, with proportions of 25.95, 20.8, 19.07, 3.98, and 1.23%, respectively. Compared to the background soils of Guangxi, the soil FMNs exhibited great enrichment in heavy metal(loid)s. The enrichment factors followed the order of Cd (243.33), Cr (49.67), Cu (5.46), Ni (8.37), Pb (23.68), Zn (15.4), and As (20.11). The heavy metal(loid)s contents in the soil FMNs of the karst areas were much higher than those observed in non-karst areas worldwide. According to the principal component analysis (PCA) results, the first three principal components contributed to about 88.81% of the total variance of the FMN compositions. PC1 (50.90%) suggested the presence of quartz, feldspar, and clay minerals-related elements in the soil FMNs, whereas PC2 (27.10%) and PC3 (10.81%) indicated the presence of Mn(oxyhydr)oxides and Fe(oxyhydr)oxides-related elements in the soil FMNs, respectively. The obtained selective extraction results demonstrated that up to 93% of the total contents of heavy metal(loid)s, namely, Cd, Pb, Cu, Ni, and Zn, were bound to Mn(oxyhydr)oxides. In contrast, oxyanionic species (As and Cr) were predominantly sequestered in Fe(oxyhydr)oxides.