Deep coal seams are increasingly considered for combined CO₂ geological sequestration and enhanced coalbed methane recovery; however, long-term reservoir integrity remains uncertain due to chemically induced weakening and intrinsic mechanical heterogeneity. In this study, the time-dependent evolution of coal integrity under supercritical CO₂ (ScCO₂)–brine interaction was systematically investigated by integrating fluid chemistry, chemical–structural characterization and spatially resolved nanoindentation analysis within a coupled chemo-hydro-mechanical (CHM) framework. Coal samples were exposed to ScCO₂–brine under simulated in-situ conditions ( \(10 \text{M}\text{P}\text{a}, 40.6 ^\circ \text{C}\) ) for varying durations. The evolution of fluid \(\text{p}\text{H}\) and oxidation–reduction potential ( \(\text{O}\text{R}\text{P}\) ) was monitored to define chemical boundary conditions. Changes in mineralogical composition and organic microcrystalline structure were quantified using X-ray diffraction and FTIR spectroscopy, while nanoindentation combined with post-indentation SEM–EDS analysis was employed to resolve localized elastic modulus and hardness responses relative to bulk medians. Results show that ScCO₂–brine interaction induces rapid early-stage acidification ( \(\text{p}\text{H} \sim 7.0 \text{t}\text{o} 5.736\) within \(3 \text{d}\text{a}\text{y}\text{s}\) ) followed by sustained redox evolution ( \(\text{O}\text{R}\text{P} 38 \text{t}\text{o} 84.33 \text{m}\text{V}\) over \(10 \text{d}\text{a}\text{y}\text{s}\) ), driving selective chemical alteration of coal constituents. These chemical processes disrupt aromatic stacking coherence ( \({\text{L}}_{\text{c}}: 10.06 \text{t}\text{o} 2.30 \text{n}\text{m}, 77\text{\%}\) reduction) and modify mechanically vulnerable functional groups without inducing graphitization ( \(<0.3\%\) change in \({\text{d}}_{002}\) ). Correspondingly, coal mechanical behavior evolves non-monotonically: early exposure produces chemically dominated, spatially uniform weakening; intermediate exposure ( \(3-5 \text{d}\text{a}\text{y}\text{s}\) ) amplifies mechanical heterogeneity through selective persistence of mineral-supported microdomains with localized elastic modulus and hardness deviating from bulk medians by up to \(\sim 60\%\) and \(\sim 80\%\) , respectively; and prolonged exposure ( \(10 \text{d}\text{a}\text{y}\text{s}\) ) leads to fracture-dominated degradation and convergence toward a uniformly weakened state. Notably, peak mechanical instability occurs during the heterogeneity-amplified stage rather than at maximum bulk weakening. This study demonstrates that bulk mechanical descriptors alone are insufficient to assess coal integrity under reactive ScCO₂ conditions. Instead, fracture sustainability and sealing performance are governed by the time-dependent redistribution and eventual collapse of load-bearing microdomains. While quantitative responses vary with coal type and geochemical conditions, the identified chemistry–structure–micromechanics framework is broadly applicable to coal reservoir stability under CO₂ sequestration.