Heavy metals (HMs) pollution is a universal and complex problem at lead smelting sites. Further understanding on the distribution, coexistence relationship and occurrence form of multi-metals in soils should be taken prior to restoration on the contaminated sites. In this study, 222 soil samples in a typical abandoned lead smelting site were investigated to understand the spatial distribution and geochemical partitioning of HMs. The results showed that soil quality was seriously threatened by As, Pb and Cd, which expressed high spatial heterogeneity. Integration of sequential extraction, X-ray photoelectron spectroscopy and mineral liberation analysers were employed to qualify the geochemical partitioning of HMs. The data showed that Pb and As were mainly partitioned in the reducible phase and residue phase, where the maximum of As were 18% and 79%, and the maximum of Pb were 31% and 64%, respectively, whilst Cd was mainly partitioned with residue phase (about 25%) and weakly acid soluble phase (about 18%). Paulmooreite was the major important mineral host for Pb and As, whereas Cd predominantly existed in willemite. These minerals containing HMs could usually with Fe reside in the octahedral layer of clay minerals such as montmorillonite, and may also reside in the interlayer. Quartz, montmorillonite and goethite were closely associated with HMs minerals in contaminated soils, which limited vertical migration of HMs and potential risks to groundwater. The results enhanced the understanding of spatial distribution and occurrence behavior of HMs, whilst providing potential benefits to heavy metal stabilization and risks control at abandoned non-ferrous metal smelting sites.