Through the large sample sampling method, 2 513 tobacco-growing soil samples in Chongqing were collected. The spatio-temporal distribution characteristics of soil exchangeable magnesium (Mg) and its influencing factors were systematically studied by applying traditional statistics and geostatistics methods. The results showed that the average content of soil exchangeable Mg was 0.88 cmol/kg, with a deficiency rate of 49.5%, a high rate of 37.3%, and a suitable rate of only 13.2%. The content of soil exchangeable Mg showed an irregular patchy distribution in space. Compared with 10 years ago, the content of soil exchangeable Mg in most tobacco-growing counties has decreased significantly. The content of soil exchangeable Mg has a moderate degree of spatial autocorrelation, and its spatial variation was mainly affected by indicators such as exchangeable calcium (Ca), organic matter, pH and soil aggregates. In guiding the application of Mg fertilizer in the tobacco-growing areas of Chongqing, attention should be paid to its spatial differences, and differentiated regional management of soil Mg should be carried out. The supply capacity of soil Mg can be regulated by using Mg-containing amendments (such as silicon-calcium-potassium-magnesium fertilizer) to adjust soil pH and applying organic fertilizer to regulate soil physical and chemical properties. This study can provide a scientific basis for the precise application of magnesium fertilizer in different regions of the tobacco-growing areas in Chongqing.