The development of highly efficient thin-film nanocomposite (TFN) membranes with superior water permeability, maintained rejection performance, and excellent antifouling capacity is critical to meeting the ever-escalating demand for fresh water. Herein, carbon dots (CDs) grafted with hyperbranched zwitterions, denoted as CDs-ZPEI0.6-10k, were first prepared by the hydrothermal treatment of citric acid in the presence of zwitterionic hyperbranched polyethylenimine (ZPEI0.6-10k) with different molecular weights (0.6, 1.8, and 10 kDa). Subsequently, the synthesized nanoparticles were introduced in membrane fabrication to form CDs-ZPEI0.6-10k-embedded TFN (TFN-CDs-ZPEI0.6-10k) membranes. The grafted shells of superhydrophilic ZPEI not only increased the chemical compatibility of CDs in the polyamide layer to suppress the formation of nonselective voids but also created a densely packed network for efficient water transportation and effective divalent salt rejection. The TFN-CDs-ZPEI10k membrane demonstrated a 2.8-fold enhancement in the permeate flux with an increased Na2SO4 rejection rate of 98.1% and improved antifouling properties than the pristine thin-film composite (TFC) membrane. This work provides an insight into the development of functionalized core-shell structured nanoparticles to effectively overcome the permeability-selectivity trade-off limitations and fouling problems in TFC membranes.