Enhancing the water flux while maintaining the high salt rejection of existing reverse osmosis membranes remains a considerable challenge. Herein, we report the use of a porous carbon nitride (C3N4) nanoparticle to potentially improve both the water flux and salt rejection of the state-of-the-art polyamide (PA) thin film composite (TFC) membranes. The organic–organic covalent bonds endowed C3N4 with great compatibility with the PA layer, which positively influenced the customization of interfacial polymerization (IP). Benefitting from the positive effects of C3N4, a more hydrophilic, more crumpled thin film nanocomposite (TFN) membrane with a larger surface area, and an increased cross-linking degree of PA layer was achieved. Moreover, the uniform porous structure of the C3N4 embedded in the ”ridge” sections of the PA layer potentially provided additional water channels. All these factors combined provided unprecedented performance for seawater desalination among all the PA-TFC membranes reported thus far. The water permeance of the optimized TFN membrane is 2.1-folds higher than that of the pristine PA-TFC membrane, while the NaCl rejection increased to 99.5% from 98.0%. Our method provided a promising way to improve the performance of the state-of-art PA-TFC membranes in seawater desalination.