Currently the range of soil degradation has been continuously expanded, and soil quality deterioration has been intensified. Particularly with the increase of environmental pollution, the risks and damages to human health caused by the entry of external pollutants such as heavy metals into the soil attracted great concern of the public. The vast majority of the external pollutants would be adsorbed by soil active components, and exposed on the soil chemical interface. Soil interfacial interactions have profound effects on the sequestration, degradation and biological metabolism of the pollutants. Therefore, focusing on the chemical behaviours of external pollutants in soil and developing soil remediation technologies to meet the social and public needs were of prime importance. To date, our understanding of the impacts of soil mineral–organic matter–microbe interactions on the behaviours of heavy metals in soils, and of an advanced model through soil-plant continuum is still relatively limited. The application of in-situ measurement, micro-examination and element tracing technologies significantly accelerated the development of studies with related to heavy metal interactions with soil active components. The in-situ measurement and the greatly improved understanding of soil microscopic properties based on microscopic spectrum laid solid foundation for the rapid understanding of immobilizing heavy metals in soil and development of soil remediation. Quantum chemistry calculation combined with spectral information has greatly enhanced the understanding of these processes at the molecular level. Meanwhile, the bioavailability and toxicity of heavy metal in soil is mostly decided by its speciation, but not by its total amount. Therefore, it is necessary to make accurate assessments of heavy metal species and speciation distribution. Geochemical models are widely used to predict the speciation and transport of heavy metals that will be important in the control of the solubility, bioavailability and the fate of heavy metals. The various types of models have been developed to calculate chemical speciation or the distribution of chemicals over all relevant forms on different soil active components. In addition, an advanced model through soil-plant continuum is also crucial to screen the trace elements from soil particle, to soil solution and plant rhizosphere. Fundamental understanding of these reactions and processes at the atomic, molecular, and microscopic levels is essential for remediation of heavy metal pollution in soils, sustaining and enhancing soil health, which includes human health, on a global scale. Future research on this extremely important and exciting area of science should be stimulated to soil pollution and remediation as well as sustain the ecosystem integrity.