Soil pollution of fluorine is a serious environmental problem in the world, and the fluorine pollution evaluation of spatial and vertical distribution study in the Karst region is quite limited. In this study, the farmland around lead-zinc mine in the Karst region was chosen as the study area. Ninety-one upper layer soil samples and two soil profiles (one in paddy field, the other one in aerated field) samples were taken. The average concentration of total fluorine of topsoil in the paddy fields is 378 mg/kg, whereas in the aerated field it is 508 mg/kg. The concentrations of total fluorine in all paddy soil samples and 97.87% aerated field soils are higher than that of the background value of Guangxi. The total fluorine contaminations in all aerated field soils are much higher than in paddy soil samples, so the aerated field is contaminated severely. The vertical distribution of fluorine is different in paddy field and aerated field. In paddy field, the content of fluorine increases from 20 to 40 cm, then it decreases rapidly from 40 to 60 cm in depth, and then increases gradually. However, in the aerated field, the content of fluorine rises gradually with the depth of the sampling point. The results of relative analysis and regression analysis between fluorine in soil and soil properties show that the spatial distribution and vertical variation of fluorine in this region are mainly affected by parent rock.