Boron content in sea water is approximately 4.5 mg/l and the rejection ratio of RO membrane is extremely less than that of other inorganic salts. On the other hand, the 1997 WHO additional guidelines for drinking water quality set the recommended guideline value at 0.5 mg/l. Recently in Japan, they set the value, restricted for the sea water desalination system, below 1.0 mg/l for standard clause which was changed from supervision guideline. However, it is unable to achieve this value constantly by single stage RO system. Hense, authors have developed the double stage RO system using sea water desalination RO membrane for 1st-stage and ultra low pressure RO membrane for 2nd-stage. Authors have simulated the flux and boron rejection of each stage and collated with the test data which was obtained through pilot plant. As a consequence of this trial, authors have led the system design which meets WHO guideline value by adjusting pH of the 2nd-stage RO feed water over 9.