Abstract: To investigate the secondary elements in Yanyuan tobacco-growing soil, the spatial variability and influencing factors of exchangeable calcium (Ca) and magnesium (Mg) were analyzed by geostatistics combined with GIS. The results showed that the average contents of exchangeable Ca and Mg were 2 507.14 and 210.66 mg/kg, respectively. Exchangeable Ca and Mg were rich in general. In spatial structure, the nugget coefficient of exchangeable Ca was 24.398%, which presented a strong spatial correlation and was mainly affected by structural factors. The nugget coefficient of exchangeable Mg was 37.293%, which presented a moderate spatial correlation and was influenced by both structural factors and random factors. Viewing from the spatial distribution angle, the exchangeable Ca content increased from east to west direction, and exchangeable Mg content increased from north to south direction. Soil particle size distribution had the greatest impact on exchangeable Ca, which explained 27.7% of spatial variability of the exchangeable Ca content, and followed by soil type, organic matter content and preceding crop. Preceding crop had the greatest impact on exchangeable Mg, which explained 15.2% of the spatial variability of exchangeable Mg content, and followed by soil particle size distribution and organic matter content.