The structures and transport dynamics of water and salt ions in polyamide (PA) reverse osmosis (RO) membranes as well as the temperature effects on the RO process were systematically investigated using a fully atomistic simulation method. By comparing the experimental data of the commercial membrane FT-30 and the available MD simulation results, the reliability of our PA RO model was validated. In addition, the groups on the polymer chains that preferentially participated in the coordination shells of salt ions were determined. Moreover, we found that the self-diffusion coefficients of both ions reduced by two orders of magnitude due to interactions between the ions and the polymer chains. Furthermore, NEMD simulations showed that the temperature has both positive and negative effects on the water flux. Although increasing the temperature can enhance the mobility of water molecule, it also can reduce the size of water clusters, which hampers an increase in the water flux. The decrease in size of the largest water clusters can partly explain the decrease in water flux when salt ions exist in the membrane. The current work provides a comprehensive understanding of the structure and transport behaviour of water and salt ions in the RO membranes.