CO2 geological sequestration is one of the prominently studied techniques for mitigating greenhouse gas emissions. However, research on CO2 sequestration in saline aquifers has predominantly focused on a macroscopic scale, with limited investigations into pore-scale mechanisms. Hence, this study employs the single-relaxation-time lattice Boltzmann method (LBGK) coupled with the (Shan-Chen) multi-component model to simulate two-phase water-gas flow in saline aquifers. The appropriate interfacial tension and corresponding G-values are determined using Laplace’s law. The transport processes of CO2 and reservoir fluids in saline aquifers are investigated, and three sequestration modes—structural trapping, residual gas trapping, and dissolution trapping—are simulated based on the pore structure of the target saline aquifer. Results indicate that the infiltration of formation water into CO2-saturated pore matrix due to hydrophilic wall effects leads to CO2 retreat, resulting in a 48.08% reduction in the overall CO2 content within the simulated pore structure. Throughout the simulation, structural trapping exhibits the highest sequestration capacity, albeit with diminishing contribution (from 89.07% to 81.95%); residual gas trapping follows with increasing contribution (from 10.92% to 16.76%); while dissolution trapping exhibits the lowest and least variable sequestration capacity (from 0% to 1.29%). The decrease in contribution of structural trapping and the increase in contributions of residual gas trapping and dissolution trapping contribute to enhanced sequestration safety.