This study combines molecular and pore-scale simulations to enhance our understanding of water, carbon dioxide (CO2), and oil flow in a porous system for high-efficiency geological carbon storage and enhanced oil recovery. We use molecular dynamics simulations to study the variation of interfacial tension (IFT), viscosity, and contact angle across varying system CO2 concentrations. The study reveals that the IFT simulation accuracy in the three-component mixture system relates positively to the volume-to-interfacial area ratio, and IFT decreases with CO2 concentration. Oil–CO2 mixture viscosity decreases and shows an intersection with water viscosity as CO2 concentration increases. The contact angle on the hydrophobic surface of kaolinite first increases and then decreases with CO2 concentration, while the hydrophilic surface contact angle is not sensitive to the CO2 concentration. Visualizing CO2 density distribution reveals its accumulation at fluid-fluid and fluid-solid interfaces and the combined effect results in the highest CO2 density at contact-line regions. Meanwhile, the elevated CO2 density at fluid-fluid interfaces reduces IFT, contributing to the initial contact angle increase, while the CO2 density increase at fluids-solid surface explains the subsequent contact angle decrease. These findings are then upscaled into a core-scale system using lattice Boltzmann simulations. The results are summarized into a phase diagram, which reveals the non-monotonic variations of the initial-residual (I-R) curves across different CO2 concentrations, and the residual saturation overall decreases with CO2 concentration for high initial saturations. These findings underscore the critical roles of system CO2 concentration and rock components, particularly kaolinite clay minerals, in subsurface multiphase seepage confronted in geological carbon storage and CO2-enhanced oil recovery, highlighting the importance of digital rock physical chemistry.