We report a molecular simulation study on porous organic cages (POCs) embedded in a lipid membrane for water desalination by reverse osmosis (RO). Four types of POC channels are examined namely straight, tilted, tilted with 3-openings and crystalline. The flow rates of water are found to increase in the order of tilted < straight < 3-opening < crystalline channel. With 3D interconnected morphology, the crystalline channel possesses the highest flow rate about 6.86 water molecules per ns. Both Na+ and Cl- ions cannot pass through the four channels with 100% salt rejection. The activation energy for water flow through the POC channels is approximately 12 - 13 kJ/mol, much lower than 22 - 26 kJ/mol through aromatic polyamide membranes. Due to confinement effect, the number of hydrogen bonds formed by water molecules in the channels is lower than in bulk water. Wetting-dewetting transition is observed in the straight, tilted and 3-opening channels, but not in the crystalline channel. This work highlights the important role of channel alignment, opening and morphology in water flow, and provides microscopic understanding of water structure and dynamics in the POC channels.