From 2017 to 2020, a total of 6 685 soil samples were collected from the plough layers (0-20 cm) of core tobacco fields in nine tobacco-growing counties in Qujing, Yunnan Province, and then pH, organic matter, hydrolytic nitrogen, available phosphorus and rapidly available potassium of the soil samples were measured. By GPS positioning, geostatistics and geographic information system (GIS) were used to investigate the status, regional variation characteristics and spatial distribution of the above soil fertility indexes. Correlation analysis and variance analysis were used to assess the effects of major factors (soil type, soil texture, climate and fertilization) on soil fertility indexes. The results showed that:soil pH ranged from 4.16 to 8.50, organic matter from 2.23 to 99.93 g/kg, hydrolytic nitrogen from 14.88 to 393.36 mg/kg, available phosphorus from 2.45 to 142.78 mg/kg, and rapidly available potassium from 19.65 to 991.33 mg/kg, with mean values of 6.30, 32.83 g/kg, 125.42 mg/kg, 29.92 mg/kg, and 270.38 mg/kg, respectively. The coefficients of variation of the above indexes were 11.59%, 33.54%, 29.93%, 64.54% and 35.18%, respectively, showing moderate spatial variation. Soil pH ranged from slightly acid to neutral, which was more suitable for growing flue-cured tobacco. The contents of organic matter, available phosphorus and rapidly available potassium concentrated in the medium to the very high levels, accounting for more than 70% of the total area of the study area. The results of semi-variance analysis showed that the spatial autocorrelation of soil pH was strong, and the variation was dominated by natural factors (soil type, texture and precipitation). The spatial autocorrelation of soil organic matter, hydrolytic nitrogen and rapidly available potassium were moderate, and their variations were affected by both natural and anthropic factors (fertilization). The spatial autocorrelation of soil available P was weak, and anthropic activities were main controlling factors that caused the spatial difference. The results of ordinary kriging interpolation revealed that spatial continuity of soil pH was good, and the overall distribution was aggregated. The strong acid and very strong acid soils were mainly distributed in Malong, Xuanwei and Huize. The distribution of organic matter, hydrolytic N, available P and rapidly available K were irregular block with strong randomness. The high value areas of organic matter, hydrolytic N and rapidly available K were mainly in Fuyuan and Luoping, while the high value areas of available P were concentrated in Luliang and Luoping.