To mitigate the “acidic and infertile” condition of purple soils in Sichuan and to address their constraints on crop productivity, a field plot experiment was conducted in Guang’an District, Guang’an City, Sichuan Province. Three fertilization regimes were designed: a 25% reduction in chemical fertilizer, substitution of 25% of chemical fertilizer with organic fertilizer, and a conventional chemical fertilizer control. Each fertilization regime was further combined with either no amendment, lime, or calcium–magnesium phosphate (CMP) fertilizer, generating nine treatment combinations. A rice–rapeseed rotation system was employed to investigate the effects of these treatments on soil properties and crop yields, with the aim of developing an acidification control and productivity enhancement technology applicable to purple soils in Sichuan. The results showed that the treatment with 25% reduced chemical fertilizer combined with CMP effectively suppressed the increase in exchangeable acidity and raised soil pH. Organic fertilizer substitution treatments increased soil organic matter, total nitrogen, and available phosphorus contents by 9.59%–43.02%, 11.34%–37.96%, and 103.90%–127.91%, respectively. After soil amelioration, rice yields across all treatments exceeded 9,800 kg/ha, with organic fertilizer substitution treatments consistently surpassing 10,500 kg/ha. Moreover, rapeseed yields under organic fertilizer substitution were 25.00%–55.08% higher than those under conventional fertilization. In summary, CMP application exhibited strong acid-suppressing potential, while organic fertilizer substitution effectively enhanced soil fertility and crop productivity. The integrated approach of “organic fertilizer substitution + CMP application” provides a practical and effective technology for ameliorating the “acidic and infertile” condition of purple parent material-derived soils in Sichuan, offering a solid scientific basis for managing acidic soils and mitigating soil acidification processes.