Display omitted •Novel TFN membranes based on polyelectrolyte nanoparticles (PNPs) were prepared.•TFN-PNP membranes exhibited high water permeability and good selectivity for amino acids.•TFN-PNP membranes had good stability and anti-fouling property in nanofiltration process. We have designed a novel type of thin-film nanocomposite (TFN) membranes with embedded polyelectrolyte nanoparticles (PNPs) and investigated their applicability in the separation of amino acids. PNP particles were mixed with piperazine (PIP) and interfacial polymerized with trimesoyl chloride (TMC), allowing for simultaneous improvement in water permeability, amino acid selectivity, and anti-fouling property. Separation performance could be conveniently tuned by modulating the chemical structure of PNPs and their content in TFN membranes, as well as adjusting the feed pH value. This work would promote the application of polyelectrolyte nanoparticles based TFN membranes in the separation and purification of amino acids.