Natural metal-bearing nanoparticles (MNPs) are of concern due to their higher mobility, potential toxicity, and the severe soil contamination in China. MNPs was usually found in contaminated environments, such as contaminated river water and soil. However, the types of MNPs from contaminated agricultural soils in China and their metal speciation were still unknown, which are important information for soil contamination prevention and remediation. We assumed that 1) the types of MNPs were relevant to the geographical location and 2) the metal speciation depended on the MNPs types. 105 samples from contaminated agricultural soils across China were collected, and MNPs were therefore extracted from these samples. The elemental compositions were determined by inductively coupled plasma optical emission spectrometry (ICPOES) and inductively coupled plasma mass spectrometry (ICPMS). MNPs categorization was achieved by cluster analysis and principal component analysis. Associations of metal contaminants with inorganic minerals and organic matter were further analyzed by Asymmetric flow field-flow fractionation (AF4) coupled with online UV-vis detector, dynamic light scattering detector, organic carbon-detector, and ICPMS. Morphology and mineralogical characteristics of MNPs were observed by Transmission electron microscope coupled with Energy-dispersive X-ray spectroscopy (TEM-EDS) and selected area electron diffraction (SAED). Elemental concentrations of MNPs exhibited regional characteristics that 1) Fe and Mn were enriched in MNPs from southeast China; 2) Ca and Mg were enriched in MNPs from southwest China; 3) Cu was enriched in MNPs from copper ore mining areas; and 4) Pb and Cd were enriched in MNPs from lead-zinc ore mining areas. All the MNPs samples were categorized into four types based on their elemental proportions: Type Ca, Type Ca-Si/Al/Fe, Type Si, and Type Si/Al/Fe. Two kinds of MNPs existed in all samples and defined as Ca-organic nanoparticle and Si-Al-Fe-organic nanoparticles according to the AF4-OCD and AF4-ICPMS results. Furthermore, Pb and As were more likely to associate with Si-Al-Fe-organic nanoparticles, while Zn, Cu, and Cd were likely to associate with both organic-Ca nanoparticles and Si-Al-Fe-organic nanoparticles. The regional characteristics and speciation of MNPs provide significantly important information for soil contamination in perspective of nanoparticle biogeochemistry.