Enriched levels of thallium (Tl) in the environment are not only derived from anthropogenic sources but also have potential natural origins owing to Tl-rich sulphide mineralization. However, little is known regarding the geochemical fractionations of Tl in contaminated soils from geogenic sources. This study aims to reveal the Tl geochemical fractionations in different types of soils from a large-scale independent Tl mine in southwestern China, via a modified Institute for Reference Materials and Measurement (IRMM) sequential extraction (four-step) scheme. The results revealed that a large percentage of Tl was related to the labile portions (including reducible, weak-acid-exchangeable, and oxidizable fraction) of the soils (68.8-367 mg kg). Further analyses by Scanning Transmission Electron Microscopy-Energy Dispersive X-ray Spectrometer (STEM-EDS) found that Tl mainly existed in the Fe-containing minerals (such as jarosite and hematite) with fine particles (∼1 μm). These results highlight that, apart from the anthropogenically induced Tl pollution, the naturally occurring Tl contamination in soils may also pose significant risks to human health and ecological safety. Owing to the relatively high mobility and bioavailability of Tl in the labile fractions, it is important to understand geochemical fractionations of this element for alleviating Tl pollution and effective management of naturally occurring Tl contaminated soils.