Supercritical CO₂-water-rock interactions significantly impact the mechanical integrity of heterogeneous conglomerate reservoirs, challenging their suitability for CO₂ sequestration and enhanced oil recovery. To evaluate these microscale mechanical and structural changes, this study uses a combination of micro-scratch testing, scanning electron microscopy, and nuclear magnetic resonance. The results reveal that the micro-scratch method enables the acquisition of a continuous mechanical property profile, addressing the limitation of traditional rock mechanics that only allows discrete point measurements. Importantly, the scratch failure modes significantly depend on the lithology of conglomerate reservoirs: Felsic and quartz conglomerates exhibit sharp grooves with interfacial shear failure, whereas debris-rich variants develop wavy, fragmented paths. CO₂-water exposure reduces the deformation resistance and causes fracture toughness to initially increase and then decline, with the most severe reduction observed in quartz conglomerates. The degradation of mechanical properties is mainly through mineral dissolution and increased porosity. The findings of this study offer key insights for optimizing storage and recovery strategies in complex reservoirs.