Carbonate rocks are widely distributed in the southwest of Qingzhou City, Shandong Province, which are an important source of soil parent material. Taking the soil in this area as the study target, selenium (Se) in rock, atmosphere and soil as well as soil properties were analyzed. The source, availability and influencing factors of soil Se were studied. The results showed that the mean content of soil total Se was 0.28 mg/kg, and most soils were sufficient in Se. The mean content of soil available Se was 15.03 μg/kg. The mean effective degree of Se was 5.70%. Available Se was significant positively correlated with the total Se. The mean content of rock Se was 0.035 5 mg/kg, which was significant positively correlated with the corresponding soil Se. The contents of soil total and available Se were significant negatively correlated with soil pH, and significant positively correlated with organic matter. Soil available Se was significant negatively correlated with clay content. The mean content of Se in atmospheric dustfall was 1.77 mg/kg, the annual settlement flux was 0.28 mg/m², the annual increment of Se in the surface soil was 0.000 9 mg/kg with an annual growth rate of 0.33%. The content of soil Se in the carbonate rock area of central Shandong is mainly controlled by the parent rock, followed by atmospheric dust. Soil physicochemical properties also have significant impacts on Se and its availability.