Boron nitride nanotubes (BNNTs) are potential candidates for water desalination owing to their advantages of higher thermal and chemical stabilities as well as resistance to oxidation. In this work, four different types of functional groups were introduced to the end of BNNT (8,8), and the mechanism of water and ion transportation through functionalized BNNTs were investigated via molecular dynamics simulation. The effect of functional groups on desalination performance of BNNT was discussed. It was found that BNNT (8,8)-COO- and BNNT (8,8)-NH3+ systems show well water flux and high ions rejection due to the space-steric effect and electrostatic interaction. Our study also revealed that the water flux in aligned functionalized BNNTs is much higher than that in reverse osmosis (RO) membranes.