The leaching and migration of potentially toxic metal(loid)s (PTMs) during stockpiling of lithium leach residue (LLR) presents a serious environmental risk. Herein, the environmental behavior of PTMs in LLR, including leaching, migration, and microbial stress response, were systematically investigated. Priority pollutants and their geochemical fractionation characteristics were identified, and effective barrier measures were proposed. The research results indicated that the concentrations of thallium (Tl) and beryllium (Be) during the leaching process exceeded the standards by 11 and 3 times, respectively, representing the primary environmental risk factors during the leaching process. Meanwhile, the leaching concentrations of nickel (Ni), cobalt (Co), and mercury (Hg) are more pronounced under neutral conditions, making these metals key focus points. The scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS) results revealed that Tl was mainly enriched in the gypsum phase, while Be might be present in the amorphous glass. In the migration behavior, the Tl content in the soil around LLR was 2.18 times higher than the background value, and the microbial community structure in the soil around LLR shifted to a dominant community dominated by Proteobacteria under the influence of PTMs. Variance partition analysis (VPA) further demonstrated that environmental risk factors, particularly Tl, contributed most strongly to the relative abundance and diversity of microbial communities, confirming that Tl is a priority pollutant for LLR. Recognizing that Tl in LLR and soil predominantly exists in the highly mobile and unstable exchangeable (Tl
Exc.
), a strategy based on the gradual conversion of Tl
Exc.
More stable reduced (Tl
Red.
) and oxidized (Tl
Oxi.
) forms can be implemented using effective physical, chemical, and biological barriers to mitigate ecological pollution from LLR stockpiles. Our work provides a detailed exploration of the environmental behavior and mechanisms of LLR, aiming to offer an effective strategy for reducing environmental pollution caused by large-scale LLR accumulation.