Interfacial polymerization (IP) and self-assembly are two thermodynamically different processes involving an interface in their systems. When the two systems are incorporated, the interface will exhibit extraordinary characteristics and generate structural and morphological transformation. In this work, an ultrapermeable polyamide (PA) reverse osmosis (RO) membrane with crumpled surface morphology and enlarged free volume was fabricated via IP reaction with the introduction of self-assembled surfactant micellar system. The mechanisms of the formation of crumpled nanostructures were elucidated via multiscale simulations. The electrostatic interactions among m-phenylenediamine (MPD) molecules, surfactant monolayer and micelles, lead to disruption of the monolayer at the interface, which in turn shapes the initial pattern formation of the PA layer. The interfacial instability brought about by these molecular interactions promotes the formation of crumpled PA layer with larger effective surface area, facilitating the enhanced water transport. This work provides valuable insights into the mechanisms of the IP process and is fundamental for exploring high-performance desalination membranes.