With the revolutionary breakthrough of high-precision mass spectrometry represented by multiple-collector inductively coupled plasma mass spectrometry (MC-ICP-MS), the research on stable isotopes has been developed by leaps and bounds. Heavy metal stable isotopes have become an effective tool to trace the circulation of heavy metals in soils, showing great application potential in identifying pollution sources, analyzing key processes, and tracking environmental behaviors. Based on the basic concept of isotopes, this paper systematically introduces the applications in using heavy metal stable isotopes to trace the source and fate of heavy metals in the soil environment, the transport and transformation of heavy metals in soil-plant system, and the environmental behaviors of metal nanoparticles. Processes influencing heavy metal stable isotope fractionation, such as redox, precipitation, dissolution, adsorption and desorption, complexation reaction, and biological action, are further summarized. Finally, the research outlook for the applications of tracing heavy metal environmental behavior by heavy metal stable isotopes is proposed, which plays a significantly important role in the prevention, control, and remediation of metal contamination in soil.