Abstract: Objective Soil fertility plays a vital role in agricultural productivity and sustainability, particularly in intensive cropping systems, such as flue-cured tobacco. This study investigated long-term changes in soil nutrient dynamics in arable lands of Yiliang County, Yunnan Province, China, from 2010 to 2022. The region’s subtropical monsoon climate, diverse soil parent materials, and continuous flue-cured tobacco cultivation have contributed to pronounced spatial variability in soil properties, highlighting the need for site-specific soil management strategies. Methods Soil samples were collected annually from the 0–15 cm depth across seven major flue-cured tobacco-growing villages using a 20 × 20 m grid sampling design. A total of 14 plots were sampled and analyzed over 13 years. Measured soil parameters included pH, organic matter (OM), and available macro- and micronutrients: Nitrogen (AN), phosphorus (AP), potassium (AK), calcium (ACa), magnesium (AMg), boron (AB), and zinc (AZ). Soil analyses followed standard methods, and statistical analyses were performed using SAS 9.4 and Python, including Pearson correlation analysis and ANOVA, to assess village-level variability in soil nutrient dynamics. Results Soil pH ranged from 4.0 to 7.5, indicating predominantly acidic conditions. Organic matter varied from 5.0 to 45.0 g/kg (mean 25.4 g/kg). Available nitrogen, phosphorus, and potassium ranged from 0.06–0.17, 0.02–0.11, and 0.10–0.50 g/kg, respectively. Significant positive correlations were observed between OM and AN (r = 0.78, P < 0.01) and between OM and AP (r = 0.65, P < 0.05), indicating the key role of OM in nutrient retention. Soil pH showed negative correlations with AN and AMg (up to r = −0.45), highlighting the adverse effect of soil acidification on nutrient availability. ANOVA results confirmed significant spatial differences among villages for most soil properties (P < 0.05–0.001). Deficiencies of micronutrients boron (AB) and zinc (AZ) were identified in southern villages. Conclusions These findings demonstrated that uniform nutrient management is ineffective in spatially heterogeneous farmland. Instead, tailored, village-specific practices, such as liming in acidic soils, organic matter enhancement in low-OM areas, and targeted micronutrient supplementation—are required. Long-term monitoring combined with precision agriculture approaches, including variable-rate fertilization and pH correction, is essential for improving soil health and supporting sustainable flue-cured tobacco production.