A new method to prepare composite nanofiltration membrane directly and efficiently by controlling the pore structure and surface morphology of the membrane is proposed in this paper. The fabrication of mesoporous silicon modified polysulfone blend membranes is via a phase inversion method. The structural morphology, surface functional group analysis, elemental analysis, hydrophilicity, chargeability, and nitrogen pollutant (ammonia nitrogen, nitrate nitrogen, total nitrogen) rejection properties of the modified membranes were found to be dependent on the amount of mesoporous silicon incorporated. The combination of the mesoporous silicon framework layer can not only effectively improve the surface structure of the modified membrane with a narrow pore size distribution but also increase the rejection of nitrogen pollutant compared with the pure NF membranes. The mesoporous material can absorb and storage the nitrogenous solution to facilitate the following interfacial polymerization, as well as induce the change of pore radius and surface structure. Compared to those pure NF composite membranes, the modified blend membranes exhibit increased water permeation flux as high as 29.09 L m−2 h−1 at 0.2 MPa. The results show that the optimum doping amount of mesoporous silicon is in the range of 0.5%-1.0%. Characterization studies demonstrated that the addition of the mesoporous silicon leads to decreased membrane pore size. Then, due to the enhanced hydrophilicity of carboxyl and hydroxyl groups on the surface, the electrostatic repulsion between the functional groups and nitrogen pollutant molecules in the membrane results in the enhanced rejection of nitrogen pollutants.