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[en] Bauxite residue often has poor physical conditions which impede plant growth. Native plant encroachment on a bauxite residue disposal area in Central China reveals that natural regeneration may improve its physicochemical properties. Residue samples collected from three different disposal ages were assessed to evaluate residue micromorphology and three-dimensional (3D) aggregate microstructure under natural regeneration. The residue aggregates in different disposal ages were divided in two sections: macro-aggregate (2–1 mm) and micro-aggregate (0.25–0.05 mm). Residue aggregate micromorphology was determined by scanning electron microscope and energy dispersive X-ray spectroscopy, and the residue aggregate microstructure was determined by synchrotron-based X-ray micro-computed tomography (SR-μCT) and image analysis techniques. Natural regeneration may improve residue aggregate stability and form a stable aggregate structure. Calcium content increased whilst sodium content decreased significantly on the surface of residue aggregates. Under natural soil-forming processes bauxite residue porosity, specific surface area, average length of paths, and average tortuosity of paths all significantly increased. This demonstrated that natural regeneration may stimulate the formation of stable aggregate structure in residues. Further understanding should focus on particle interaction forces and agglomeration mechanisms with the addition of external ameliorations. - Highlights: • Weathering improved physico-chemical properties of bauxite residue and changed micromorgrophy of residue aggregates. • Weathering stimulated the formation of stable aggregate structures in residues. • Weathering changed aggregate microstructures, including pore throat and shape parameters.