As emerging micropollutants (EMPs) become a global environmental concern, it is crucial to devise energy-efficient methods that can effectively remove EMPs from water. Polyamide thin-film composite (PA-TFC) membranes are state-of-the-art water separation membranes and their applications for EMPs separations have been increasingly conscripted in recent years. However, a comprehensive fundamental understanding of the underlying relationship between membrane microstructures and EMPs transport across the PA-TFC membranes remains enigmatic. To address this gap, we thoroughly investigated the separation behaviors of two PA-TFC membranes with distinct PA microstructures toward a wide spectrum of EMPs with various dimensions and chemistries. By reconciling experimental evidence and density-functional theory (DFT), we disclosed that the water permeance of the PA-TFC membrane is predominately governed by the effective filtration area associated with surface protuberances and the intrinsic wall thickness of the PA microlayers. Precise control of the solute–PA interactions is explicitly important for membrane selectivity toward EMPs, which deserves more attention in future membrane design besides synchronously regulating membrane pore size and size distribution. This work represents a conspicuous step forward in the fundamental understanding of the structure–performance relationship of PA-TFC membranes for EMPs separations, which would inspire the rational construction and structural regulation of high-performance membranes for new pollutants removal.