A complexation-enhanced boron removal method in a dual-stage nanofiltration (NF) seawater desalination process was investigated. A comparative experiment of five different polyols was carried out. Sorbitol was chosen as the complexation additive because of its higher equilibrium constant. The reaction between boron and sorbitol was rapid and only slightly affected by the other ions. Due to the complexation reaction, boron rejection of dual-stage NF seawater desalination process was increased from 35% to 62% in the first stage and from 42% to 55% in the second stage. Boron concentration reached 0.1mg/L by adjusting the complexation and pH value. Molecular structures were simulated using the molecular simulation technology. The results indicated that molecular structure and molecular size played significant roles in enhancing boron removal. Meanwhile, NaOH and sorbitol had no evident effect on the chemical structure of the membrane surface. The results indicated that complexation is an effective method to reduce boron concentration in a dual-stage NF seawater desalination process.