Aromatic polyamide (PA) membranes fabricated from interfacial polymerization are widely used for desalination and water treatment. The fabrication of the high-flux PA membrane requires a fundamental understanding of the molecular mechanisms of water dynamics in the PA, which is still obscure due to the limited experimental methods. Herein, molecular dynamics (MD) simulations were employed to establish an atomic model of ultrathin free-standing PA membranes with various thickness and to explore the thickness-dependent dynamics of water molecules in the PA membrane. Simulation results illustrate that the simulated PA membrane has an average pore radius of 3 A similar to the free volume size of the experimental PA membrane measured by PALS. The PA could be identified as the swelling layer (SL) and the confined layer (CL) based on their water diffusion rates. The diffusivity of water in the confined layer of PA membrane was much lower than that in the swelling layer and thus determined the water flux of the PA membrane. The water diffusivity in the sub-8 nm PA membrane is greatly enhanced due to a very thin confined layer thickness, illustrating the mechanism of the experimentally fabricated sub-8 nm PA membrane having the dramatically enhanced water permeability. Furthermore, results show that water molecules tend to transport rapidly in the free space inside the PA membrane. Our results provide some insights into the thickness-dependent water dynamics in the PA on a molecular level and may help to design the next generation of high-flux PA membranes.