Reverse osmosis (RO) desalination has become an efficient approach to alleviate the freshwater scarcity, and various two-dimensional (2D) nanomaterials are widely exploited as RO membranes. Due to excellent chemical stability and high flow rate, molybdenum diselenide (MoSe2) has shown great potential in water treatment applications. However, the microscopic understanding of desalination mechanism is still lacking. In this study, by using in silico approach, the high-efficiency desalination performance of layer-stacked MoSe2 nanochannels was investigated. The simulation results reveal that the edge chemical properties and spacing of MoSe2 nanochannels have significant effects on the desalination. Increased spacing can increase the permeability of water but reduces ion rejection. In particular, the permeability through the Mo–Se channel with 8 Å spacing achieves a value of about 3.1 × 10−5 kg m m−2·h−1 bar−1 along with 100 % ion rejection rate, which is several orders of magnitude higher than that of traditional commercial membranes. This indicates that the MoSe2 nanochannels are superior for seawater desalination. In addition, the underlying mechanism of water passage through the MoSe2 channel are investigated by analyzing the potential of mean force, the 2D density of water molecules, and the hydrogen bonding inside the nanochannels during transportation. The results suggest that layer-stacked MoSe2 membrane can be used as a desired RO membrane for efficient seawater purification, which facilitates the design of future filtration membranes.