Soil serves as the primary repository of trace elements required for tobacco growth, making it crucial to investigate the plentiful-lack index and the factors influencing the abundance of these trace-elements in soil used for tobacco cultivation. Therefore, this study utilized the findings from two soil surveys conducted in 2005 and 2018 within Fujian Province’s tobacco-planting soil, employing geostatistical analysis methods to examine the spatial and temporal variability characteristics and the driving factors affecting the trace elements (Fe, Mn, Cu, Zn). The study revealed that over the 14 years period from 2005 to 2018, there was a noticeable fluctuation in the trace element content of soil, yet all remained at either high or extremely high levels. Upon further analysis, it was found that the available iron content in Fujian Province’s tobacco-planting soil in 2018 predominantly ranged from 200-350 mg/kg (83.90%), with distribution mainly influenced by non-structural factors; the available manganese content predominantly fell within the range of 10-25 mg/kg (90.14%), primarily influenced by structural factors; the available copper content was primarily concentrated in the range of 1.5-3 mg/kg (80.44%), influenced by a combination of structural and non-structural factors; the available zinc content predominantly ranged from 1.5-4 mg/kg (91.88%), exhibiting a spatial auto-correlation pattern similar to that of the soil available copper; correlation and stepwise regression analyses revealed that soil pH and organic matter directly influenced the content of soil trace elements, whereas soil exchangeable magnesium had an indirect effect on these elements through its impact on pH. In the tobacco-planting regions of Fujian Province, trace-element deficiency such as Fe, Mn, Cu, Zn was essentially non-existent, with overall contents being high. Amidst the acidic soil conditions prevalent in Fujian Province, fertilizers such as magnesium hydroxide, magnesium oxide, and calcium magnesium phosphate could be utilized as alternatives to magnesium sulfate for managing soil trace elements.