Hydrogen has been regarded as an important clean energy source in recent years. The depleted reservoir has been recognized as an economic geological site for hydrogen storage as a result of its large storage capacity. However, the caprock sealing safety of the reservoir must be considered before underground hydrogen storage. To investigate the hydrogen loss in the caprock, we have studied the H 2 dissolution in the caprock water-saturated kaolinite nanopores using molecular simulations in this work. The H 2 /CH 4 mixture dissolution in the caprock nanopores was also studied to investigate the effect of the CH 4 cushion gas on the H 2 dissolution. The results showed that the H 2 dissolution can increase by up to 27 times the bulk solubility under the impact of nanoconfinement enhancement, and the gas loss through the caprock is mainly by the smaller water-saturated pores. The maximum solubility of H 2 and CH 4 occurs at the 0.55 and 0.6 nm pores, respectively. For the 0.5−0.55 nm pores, the dissolved H 2 density exceeds CH 4 at the H 2 fraction above 50%. As the pore size increases to 2.0 nm, the H 2 and CH 4 solubility is comparable as the nanopore confinement effect gradually becomes weak. However, as the H 2 fraction increases to 80%, the H 2 dissolution dominates over CH 4 , even in the 2.0 nm pore. With the increase of the pore size, the water molecules gradually occupy the strong adsorption sites near the surfaces; thus, the gas molecules start to accumulate in the pore middle. The cushion gas of CH 4 adopts various molecular angles in the pores, which are 50°and 130°in the 0.55 nm pore and tripod and inclined angles of 70°and 110°in the 1.0 nm pore. However, the dissolved H 2 molecules are always perpendicular toward the pore surface, which is not affected by the pore size and water molecules. Under the influence of brine, the solubility of H 2 and CH 4 decreases and the impact of brine is more noticeable in larger pores. The high brine salinity helps to reduce the H 2 loss in the caprock nanopores.