Soil acidification threatens to agricultural sustainability by increasing phytotoxic exchangeable aluminum ions (Al3+). Developing sustainable soil amendments is essential to address the limitations of conventional additives, such as soil compaction, re-acidification, and high application costs. This study evaluated the potential of calcium lignosulfonate (LC) and phosphogypsum (PG), two industrial by-products, as alternatives to lime for mitigating soil acidification and improving fertility in acidic yellow and purple soils under pot experiments. Molecular modeling was applied to elucidate the mechanisms of LC functional groups in Al3+ immobilization. The results revealed that LC + PG increased soil pH by 0.66 and 1.10 in yellow and purple soils, respectively, compared with Lime. LC + PG significantly reduced exchangeable Al3+ by up to 91.40 % compared with conventional fertilizer (CK, p < 0.05). LC + PG significantly increased soil organic matter by up to 22.36 %, exchangeable base ions by up to 110.74 %, and 100-grain weight by 22.04 %-225.37 % compared with CK (p < 0.05). Furthermore, LC + PG increased the relative abundance of Actinobacteriota by 1.67 % and 3.52 % compared with CK and lime, respectively. Molecular modeling indicated that hydrophilic LC groups facilitated Al3+ immobilization and enhanced interactions with soil enzymes via electrostatic adsorption, electron transfer, and hydrogen bonding. These findings emphasize the superior synergistic effect of LG + PG in mitigating soil acidification, improving soil fertility, and restructuring microbial communities compared with lime. This study provides valuable insights for the reuse of industrial by-products, cost-effective soil amendments, and sustainable soil management practices.