Based on the analysis of thallium content in floodplain soil samples obtained by the China Geochemical Baselines project in Three Rivers regions of southwest China, the pollution status of the thallium in soil of the study area was comprehensively evaluated by multiple methods. Results showed that, the thallium content in top soil of the region was 0.17~2.65mg/kg with the mean of 0.80mg/kg and the coefficients of variation was low, which was slightly higher than soil background value of China and slightly lower than that in deep soil. The characteristics of thallium content in the top/deep soil were mainly controlled by the natural geological background, and its overall trend was north was higher than south, and west was higher than east. Based on the background of related elements of soil in different parent rock areas in China, the parameters of enrichment coefficient, geoaccumulation index, potential ecological risk with the mean 1.30, -0.41 and 12.48, respectively, and non-carcinogenic health risk assessment with hazard quotient less than 1 all showed that the thallium contamination level of soil in the study area was generally low and there was no non-carcinogenic health risk of heavy metal of thallium in the soil, which essentially reflected that there had the characteristics of low pollution and low health risk of thallium pollution in soil of the study area under the control of natural geological background. Meanwhile, there was a certain amount of man-made pollution with a tendency of north was lighter than south, and west was lighter than east in the study area, reflected by the distribution characteristics of thallium content of soil in different land use field and the ratio of thallium content in top and deep soil. Comprehensive analysis showed that, the mining activities related to lead and zinc minerals in the study area might be the main source of man-made thallium pollution. Some parts of the study area had a certain degree of pollution and potential health risks due to the superposition of man-made pollution and natural geological background, including the south of Drung river basin, south central Nujiang river basin, the north and south Lancang river basin and south central Yuanjiang river basin, and these areas should attract people's attention to thallium pollution in soil. © 2021, Editorial Board of China Environmental Science. All right reserved.