The instability of most metal organic frameworks (MOFs) in water limits their application in seawater desalination. The fluorinated metal organic framework has a suitable pore size and excellent water stability and is expected to be a new generation desalination material. In this work, the desalination performance of FMOF-1 and FMOF-CH3 was evaluated by non-equilibrium molecular dynamics simulation. The water permeability is 16.18 L·cm−2·day−1·MPa−1, which is one to two orders of magnitude greater than that of conventional reverse osmosis membranes, and the ion rejection is greater than 95%. At the same time, the effect of different hydrophobic groups in FMOF membranes on desalination was explored, and the transport mechanism of water molecules passing FMOF membranes was further investigated.