The desalinated water obtained by the water treatment process based on the membrane is attracting a lot of attention as a promising technology that can solve the global water shortage problem. Reverse osmosis membrane-based desalination, one of the most widely used desalination processes, is a technology that desalinates abundant seawater on Earth, thus having great potential in the desalination industry. To improve the performance of the desalination process, it is necessary to understand the reverse osmosis mechanism of the membrane at the atomic/molecular level. In this review, we introduce molecular simulation, which plays an important role in material research today, and the roles of computational simulation at the atomic/molecular level in the development of reverse osmosis membranes.