Cropland acidification seriously restricts sustainable agricultural development. The main purpose of this study was to determine whether deeper tilling could alleviate topsoil acidification to improve the quality of arable land. A soil column incubation experiment simulating tillage depths (10 cm, 30 cm and 50 cm) and lime addition was conducted to determine their effects on soil acidification improvement. The changes in soil pH, exchangeable acidity, ammonium nitrogen (NH₄⁺-N), nitrate nitrogen (NO₃⁻-N), available phosphorus (AP), and microbial phospholipid fatty acids (PLFA) were analyzed. Tillage depth, lime application, and their interaction all had significant impacts on soil pH. T50 (simulated tillage depth of 50 cm) and T50+Lime (simulated tillage depth of 50 cm plus lime) treatments significantly increased the topsoil pH from 5.41 to 6.35 and 7.12, respectively. T50 treatment significantly reduced the soil exchangeable acid content compared to the T10 treatment. The nutrient accumulation along soil column indicated that the T50 and T50+Lime treatments significantly increased NO₃⁻-N and AP content in the >30–50 cm soil layer. Compared with T30, NO₃⁻-N accumulation in the >30–50 cm soil layers of T50 and T50+Lime treatments was 6.62 and 7.93 times higher, respectively. The accumulation of AP in the >30–50 cm soil layers of the T50 and T50+Lime treatments was 1.33 and 1.54 times higher than in the T30 treatment, respectively. These findings imply tillage up to 50 cm without exogenous materials could be a potential measure to reduce topsoil acidification and increase nutrition availability of >30–50 cm soil layers. Tillage of up to 30 cm combined with lime application confers greater benefits, which would particularly impact crops with shallow root systems. Subsequent field experiments will be conducted to further investigate the efficacy of these strategies in enhancing crop yield.