Iron (Fe) minerals are widely distributed in soil and are an important component of soils, which play an important role in regulating soil health, pollutant behavior, and element biogeochemical cycles. These minerals are of great importance since they can influence many key chemical processes. For instance, they can affect the bioavailability and toxicity of heavy metals via a series of physical and chemical processes, such as physical encapsulation, adsorption, complexation, and co-precipitation. Additionally, soil organic substances can affect the transformation of iron minerals and lead to changes in the structure and surface properties of the products. Besides, the resultant products of such interactions have been reported to show a varied affinity for heavy metals and demonstrate contrasting effects on the environmental behaviors of heavy metals. In this review, we considered the following three points:(i) the effect of reaction pH, reaction temperature, and the added ferrous iron activity and concentrations on the abiotic transformation rates, degree, and pathways; (ii) the influence of soil root exudates such as oxalate acid, citric acid, and phenols on the accumulation, reduction, nucleation, dissolution and coprecipitation of Fe oxides; and lastly (iii) the surface complexation, and redox reactions of heavy metals at iron minerals-water interface. Here, the influence of iron mineral transformation on (a) the distribution of heavy metals, (b) the reaction process and molecular mechanism of heavy metals at the interface of iron mineral-organic matter, and (c) the use of kinetic models to evaluate and predict the environmental behavior of heavy metals is given in detail. It was observed that the ferrous oxidation is mediated by anaerobic photoautotrophic ferric oxidizing bacteria, and the bacteria affect the iron oxidation process through nitrate-reducing ferrous oxidation and biomineralization. Also, iron-reducing bacteria influence the iron reduction process primarily through chelating reagents, redox-active electron shuttling substances, and the c-type cytochrome of the outer membrane. Additionally, soil organic matters (e.g., fulvic acids and humic acids) can affect the aggregation and stability of soil aggregates. They can interact with iron minerals packaged in soil aggregates by electrostatic attraction, coordination exchange, van der Waals force, hydrophobic interaction, and hydrogen bonding, thereby affecting the biotic and abiotic transformation process of iron minerals. Nevertheless, this study can only serve as a reference for detail understanding of iron mineral-organic matter-heavy metal dynamic interaction mechanism at the microscale and the interaction molecular mechanisms of heavy metal at the soil multi-component interface. We suggest that future researchers should provide (i) an in-depth analysis revealing the molecular mechanism of the soil heavy metals environmental behavior under the dynamic interaction of iron minerals, soil organic matter and microorganisms, (ii) a clear picture of the soil interfacial reaction processes and mechanism at the atomic and molecular level, and (iii) a path for developing an in-situ dynamic monitoring method and technology for soil-water interface reaction process in the microscale, simulating the complex biogeochemical reactions, and predicting and assessing the trend of heavy metals in the complex natural environment by coupled kinetics models.