• Combined desulfurization gypsum and maize straw-P. oxalicum effectively reduced saline-alkalinity and altered aggregate-associated chemical binding agents in bauxite residue.
• Maize straw-P. oxalicum specifically stimulated the formation of water-stable macroaggregates with enhanced erosion resistance.
• Exchangeable polyvalent metal ions, pyrophosphate extractable Fe oxide, and organic carbon were positively correlated with long-term aggregate stability.
• The results provide practical data support for ecological restoration and soil formation in bauxite residue disposal areas.