Due to the relatively low reactivity of hydroxyls with acyl chloride groups, the synthesized polyester (PE) membranes commonly have loose structures, only capable of removing large-molecule organics with low rejection of inorganic salts. In this study, the pore size reduction of the synthesized PE membrane was successfully achieved by optimizing the interfacial polymerization (IP) reaction between erythritol and trimesoyl chloride (TMC). The optimized membrane was able to maintain a high xylose rejection (∼60 %) and acceptable water permeance (7.85 L m−2 h−1 bar−1), which was suitable for drinking water treatment. Through comprehensive characterizations, a two-stage membrane formation process was demonstrated regarding the reaction between aqueous monomers with different reactive functional groups and TMC. The highly reactive primary hydroxyls more preferentially participated in the initial reaction stage, leading to a linear cross-linking pattern of polyester. When the molecular diffusion was inhibited, the participation of secondary hydroxyls made the reaction proceed toward partial or full cross-linking. The distinct roles of the two kinds of hydroxyl groups were further verified by the energy barrier differences obtained by density functional theory (DFT) calculation. The exploration of membrane-optimized preparation and formation mechanisms can promote the structural regulation and tailored synthesis of PE membranes for various applications.