Since the water permeation mechanisms of polyamide membranes are highly dependent on the micro-structure of polyamide membranes, a deeper understanding of the formation process of them is necessary for the optimization of the membrane performance. As most simulation works construct the polyamide membranes in an ideal way, the interfacial diffusion of monomers, which is crucial for the formation of polyamide membranes, is usually ignored. To address this issue, we mimic the experimental conditions to develop an atomic model of a highly crosslinked polyamide membrane by conducting molecular dynamics simulations. Via tuning the concentration and molar ratio of monomers, the diffusion of monomers and its influence on the subsequent reaction are altered, and the final membrane structure consequently changed. Simulation results reveal that increasing the trimesoyl chloride concentration results in thicker membranes with a reduced specific surface area and consequently decreased water permeance. On the other hand, increasing the m-phenylenediamine concentration will accelerate the reaction rate and reduce the final crosslinking degree. A deeper understanding of the mechanism of polyamide-membrane formation is unveiled in this work, which can aid in the design of high-performance polyamide membranes in the future.