CO₂ sequestration in coal seams represents an effective strategy for mitigating CO₂ emissions. However, the complicated interaction of CO₂-water-coal at the micro-scale may compromise the structural integrity and mechanical strength of coal, thereby adversely impacting the efficacy and safety of CO₂ sequestration in coal seams. This study introduces a novel indentation testing method that reveals the scale-dependent evolution mechanisms of coal microstructures, enabling the accurate and reliable quantification level of degradation in the micromechanical properties caused by supercritical CO₂-water-coal interactions. Using this method, the extent of mechanical degradation in three types of coal microstructures could be accurately evaluated under supercritical CO₂-water-coal interaction. The pure organic matrix exhibited remarkable stability under all fluid treatments, with minor changes in microstructure feature and a mechanical property reduction of less than 25%. In contrast, the mineral structures were significantly altered by treatment with fluid mixed with supercritical CO₂ and brine, with erosion depths and mechanical property reductions reaching 1.6 µm and 80% in granular structures, and 6.4 µm and 90% in banded structures. However, in the absence of brine or supercritical CO₂, the erosion depths and mechanical property reductions of fusinite were limited.