Polyelectrolyte complex nanoparticles (PEC NPs) armed with tunable quaternary ammonium groups are designed from dextran sulfate sodium and chitosan (CS), and utilized as novel building blocks to prepare quaternized polyelectrolyte complex membranes (QPECMs) for nanofiltration process via surface coating and glutaraldehyde crosslinking method. Structural characteristics, surface properties and separation performance of QPECMs are compared with these of quaternized CS membrane (QCSM) and nascent PEC NPs membrane (PECM). Results indicate that increased water permeability of QPECMs generates from loose aggregation architecture moderating tight packing of polymeric chains, while enhanced ion selectivity is attributed to efficient charge character providing strong electrostatic repulsion toward metal cations. Moreover, QPECM-4 features efficient anti-scaling properties with low flux decline ratio of 11.5% and high recovery ratio of 96.5%, accompanied with long-term stability and recyclability in gypsum dynamic filtration. This design strategy of water-soluble PEC NPs serving as building blocks presents facile adaptability to other polyelectrolyte complex membrane systems for specific water treatment and environmental remediation.