Selenium (Se) and arsenic (As) contaminations in surface and ground water have become a perilous issue worldwide in recent years. In order to remove them proficiently and simultaneously, sodium ion modified carbon quantum dot (Na-CQD) incorporated thin-film nanocomposite (TFN) membranes have been developed. Na-CQDs with an ultrafine size of 3.2 nm were synthesized from the pyrolysis of citric acid via a simple thermal treatment and then participated in the formation of polyamide (PA) layer during interfacial polymerization. The new Na-CQD modified TFN membranes exhibit enhanced pure water permeability (PWP) and rejection rates for toxic ions due to their higher surface hydrophilicity and reduced pore sizes compared to the original thin-film composites (TFC) membrane. Among them, the novel TFN membrane containing 0.05 wt% of Na-CQDs (TFN-0.05) displays the highest PWP of 10.4 LMH/bar and impressive rejections of 97.5%, 98.2% and 99.5% toward SeO32-, SeO42- and HAsO42-, respectively. In the simultaneous separation of Se and As, better ion rejection results are obtained. Meanwhile, the TFN-0.05 membrane validates superior antifouling propensity and robust long-term stability under the 180-h test. This study may deliver valuable insights in the preparation of nanoparticle modified polymeric membranes for water purification.