To provide a theoretical basis for targeted management of magnesium nutrition in tobacco-growing soils in Chongqing, 2513 soil samples were collected. Traditional statistical and geostatistical methods were applied to analyze the spatial and temporal distribution of soil available magnesium content and its influencing factors in Chongqing tobacco-growing areas. The results showed that the average soil available magnesium content in Chongqing tobacco-growing soils was 0.88 coml/kg. The proportion of soil exchangeable magnesium deficiency reached 49.5%, while the proportion of excess magnesium was 37.3%, and the suitable proportion was only 13.2%. There was a coexistence of magnesium deficiency and excess in the tobacco-growing soils of Chongqing. The spatial distribution of soil available magnesium content showed concentrated patches and patchy distribution, while the temporal distribution showed an initial increase followed by a significant decrease. The soil exchangeable magnesium content had a moderate degree of spatial autocorrelation, and its spatial variation was influenced by both structural and random factors. Factors such as altitude, parent material, soil type, soil pH, exchangeable calcium, total nitrogen, and organic matter content were all important factors affecting the exchangeable magnesium content in tobacco-growing soils. Therefore, in guiding the application of magnesium fertilizers in Chongqing tobacco-growing areas, attention should be paid to their spatial heterogeneity. Scientific zoning management of soil magnesium should be conducted, and soil pH can be adjusted through the use of magnesium-containing amendments (such as silicon-calcium-potassium-magnesium fertilizers) and soil physicochemical properties can be regulated through the application of organic fertilizers to improve soil magnesium supply capacity. This can provide a scientific basis for the management of tobacco cultivation and the precise application of magnesium fertilizers, as well as the production of high-quality tobacco leaves in Chongqing.