Geostatistics, GIS, and fuzzy mathematics methods were used in this study to systematically investigate and analyze soil fertility status and its spatial variability characteristics in the Baihetan hydropower project area. The results showed that available nitrogen (AN) and rapid available phosphorus (RAP) had strong spatial variability, organic matter (OM) and rapid available potassium (RAK) had moderate spatial variability, while cation exchange capacity (CEC) and bacterial community α diversity index (Chao1) variation coefficients were the smallest and had weak spatial variability. The average values of AN, OM, CEC, RAK, RAP and Chao1 were 14.08 mg/kg, 14.02 g/kg, 8.04 cmol/kg, 98.53 mg/kg, 0.65 mg/kg and 0.97 in 0–10 cm depth, 12.14 mg/kg, 12.70 g/kg, 8.02 cmol/kg, 109.78 mg/kg, 0.74 mg/kg and 0.93 in 10–20 cm depth, respectively. The average contents of AN and RAP were lower than the 6^th levels, OM and CEC were at the 4^th levels, and RAK was at the 3^rd level of soil property classification standard. 10–20 cm RAK showed weak spatial autocorrelation, while AN, OM, CEC, 0–10 cm Chao1, and 10–20 cm RAP had nugget coefficients less than 25% and showed strong spatial autocorrelation. Integrated soil fertility index (IFI), AN and OM gradually decreased from northwest to southeast, while other fertility indicators had different spatial distribution characteristics. In conclusion, the overall soil fertility level was low in the study area, with RAP and AN as the main limiting factors.