Soil contamination by heavy metals in China is one of the serious environmental problems, and molecular-level understanding the interaction mechanisms of heavy metal with soils facilitate our precise management of contaminated sites. Organo-mineral complexes, as one of the significant soil components, widely distributed in the soil systems, and the interaction mechanisms of heavy metals with organo-mineral complexes remains unclear due to their complexity and heterogeneity. In this study, batch experiments were conducted and multiple synchrotron-based hard and soft X-ray techniques (XRF, XAS, STXM etc.) were applied to characterize the microstructures of organo-mineral complexes, synthesized from model systems and fractionated from agricultural soils, and the distribution and molecular speciation of their associated heavy metals under the micro- and sub-micro spatial scales. We found the significant impact of soil organic matter on the binding mechanisms of heavy metals with organo-mineral complexes, which depends critically on the contents and molecular structures of soil organic matter. This study provides new insights into the interactions mechanisms of heavy metals with soils, which benefits our comprehensive understanding of the environmental behaviors and availability of heavy metals in contaminated soils.