The incorporation of nanofillers in interfacial polymerization is a promising approach to elevate the permeability of thin-film nanocomposite (TFN) membranes. However, commonly-used inorganic nanomaterials (e.g., silica, zeolites, and carbon nanotubes) often bring defects, and thus low selectivity to the membranes due to their poor interfacial compatibility with polymeric matrix. In this work, organic polydopamine/poly(ethylene glycol) (PDA/PEG) nanocapsules were designed as fillers of the TFN membranes prepared by interfacial polymerization of piperazine with trimesoyl chloride. No aggregation phenomenon was observed for the nanocapsules in the membranes, which is attributed to their good dispersity brought by the grafted PEG brushes on the shells. Defect-free separation layer was obtained for the TFN membranes due to good miscibility of polymeric nanocapsules with polyamide matrix. The inner cavities of the embedded nanocapsules played a role of shortcuts for water permeation through the thin-films. The resultant PDA/PEG-TFN membranes showed a high water permeance of 11.7 L.m(-2).h(-1).bar(-1), approximately 2.2 times that of the control TFC membrane, while maintained high solute rejections (RNa2SO4 = 95% and R-Vitamin (B12) = 98%). Moreover, the PDA/PEG-TFN membranes exhibited high selectivity towards di-/mono-valent salts. This work presents a novel strategy of constructing water transport channels in selective layer to develop high performance nanofiltration membranes.