The hydrogenation of nitroaromatics to prepare aromatic amines plays a crucial role in the chemical industry. Traditional hydrogenation has the risk of hydrogen leakage from the equipment, and its catalyst has the disadvantage of being easily deactivated and difficult to recover. In this study, we designed an efficient and stable mesoporous catalyst, Pd@SBA-15, which was constructed by impregnating the nanopores of the mesoporous material SBA-15 with palladium nanoparticles. The catalyst was then filled in a micro-packed-bed reactor (MPBR) for continuous flow hydrogenation. The designed continuous flow hydrogenation system has two distinctive features. First, we used mesoporous Pd@SBA-15 instead of the traditional bulk Pd/C as the hydrogenation catalyst, which is more suitable for exposing the active sites of metal Pd and reducing the agglomeration of nanometals. The highly ordered porous structure enhances hydrogen adsorption and thus hydrogenation efficiency. Secondly, the continuous flow system allows for precise detection and control of the reaction process. The highly efficient catalysts do not require complex post-treatment recovery, which continues to operate for 24 h with barely any reduction in activity. Due to the high catalytic activity, the designed mesoporous Pd@SBA-15 showed excellent catalytic performance as a hydrogenation catalyst in a continuous flow system with 99% conversion of nitroaromatics in 1 min. This work provides insights into the rational design of hydrogenation systems in the chemical industry.