The size of soil particles can significantly affect the enrichment of heavy metals in soil. However, the size effect of soil particles in colloidal dimension on the partitioning and geochemical fractions of heavy metals has been rarely studied. In this study, four soils, polluted by several heavy metals, were collected from Jiangxi (JX) and Hebei (HB) Provinces and Guangxi Zhuang Autonomous Region (GX and GX′) in China, respectively. Five size fractions (>10, 10–1, 1–0.45, 0.45–0.2 and <0.2μm) were separated from the studied soils to investigate the partitioning and geochemical fractions of cadmium (Cd), cadmium (Cr), copper (Cu), manganese (Mn), nickel (Ni), lead (Pb) and zinc (Zn). For JX, GX and GX′ soils, Cr and Ni in JX and GX′ soils and Cr, Ni and Mn in GX soil, as geogenic elements, were comparable with their background values; whereas other heavy metals, as anthropogenic elements, were higher than their background values. For the HB soil that was only polluted by Pb, Cd, Cr, Cu, Mn, Ni and Zn were the geogenic heavy metals. Generally, the contents of most heavy metals in the soil colloids were higher than that in coarse soil particles, and the partitioning tendencies with particle size were not significantly different between geogenic heavy metals and anthropogenic heavy metals. The partitioning of heavy metals in various soil particle size fractions was closely related to the soil particle compositions, such as OM, Fe/Al oxides and clay minerals. For geogenic heavy metals (Cr, Ni), the proportion of the residual fraction, which is imbedded in the silicate crystalline structures of soil particles, was very high, and the geochemical fraction patterns of the various soil particle size fractions were comparable, whereas the bioavailable fraction of anthropogenic heavy metals, such as Cu, Mn, Pb and Zn, decreased with decreasing soil particle size and the proportion of other fractions increased with decreasing size. This result indicates that more anthropogenic heavy metals exist in their stable form in fine soil particles. Correlations between Fe, Al and TOC and the bioavailable fraction of anthropogenic heavy metals were all negative, and most were significant or very significant indicating that high contents of OM and Fe/Al oxides stabilize anthropogenic heavy metals in fine soil particles.