Abstract: To address nutrient depletion and imbalance caused by soil acidification in the rice-rapeseed rotation system in the red soil region of southern China, this study was conducted in typical acidic paddy fields in Xiangtan County, Hunan Province. A field plot experiment was carried out to systematically investigate the effects of different fertilization regimes on crop yield and soil fertility. Four fertilization treatments were established: conventional fertilization (T1, chemical fertilizer applied alone in both rice and rapeseed seasons), soil quality improvement mode (T2, rapeseed season: chemical fertilizer combined with organic fertilizer replacing 30% of nitrogen and lime; rice season: chemical fertilizer combined with organic fertilizer replacing 30% of nitrogen), productivity enhancement mode (T3, rapeseed season: specialized rapeseed fertilizer combined with medium and trace elements; rice season: chemical fertilizer combined with silicon fertilizer), and the synergistic improvement mode of soil quality and productivity (T4, rapeseed season: specialized rapeseed fertilizer combined with organic fertilizer replacing 30% of nitrogen, medium and trace elements, and lime; rice season: chemical fertilizer combined with organic fertilizer replacing 30% of nitrogen and silicon fertilizer). The results showed that the T4 treatment performed best in terms of both crop yield improvement and soil amelioration. Compared with T1, rapeseed yields under T2, T3, and T4 increased by 27.1%, 46.7%, and 58.2%, respectively, while rice yields increased by 5.6%, 10.3%, and 18.5%, respectively. In addition, the T4 treatment increased soil pH by 0.58 and 0.59 units in the rapeseed and rice seasons, respectively, and significantly enhanced soil organic matter, total nitrogen, available potassium, as well as microbial biomass carbon and nitrogen contents in either the rapeseed or rice season. Evaluation based on the Soil Quality Index (SQI) indicated that the comprehensive soil quality under the T4 treatment was significantly superior to that under the other treatments, with a consistent ranking of T4 > T2 > T3 > T1 across both seasons. Correlation analysis revealed that rapeseed yield was significantly and positively correlated with soil organic matter, total potassium, available potassium, total nitrogen, and nitrate nitrogen contents, whereas rice yield was significantly and positively correlated with soil pH, organic matter, total nitrogen, total potassium, available potassium, and microbial biomass carbon content. In conclusion, the integrated fertilization regime T4 can effectively and synergistically enhance crop yield in the rice-rapeseed rotation system, alleviate soil acidity constraints, and improve soil fertility, providing a feasible fertilization management strategy for promoting green and sustainable agricultural development in the red soil regions of southern China.