Large size interstices of carbon nanotube arrays have been proved to exhibit extremely higher water permeation. However, ion retention is still a big problem if the gap is to be used in desalination. Herein, nonequilibrium molecular dynamics simulations were applied to investigate water and ions transport among the different-size (9 Å, 11 Å, 13 Å, and 15 Å) interstices of outer wall membrane of the (10, 10) CNT array. Modifications were performed to improve salt rejection. The modifications included different lengths and types of carbon chains with hydrophilic COO– or NH3+. Simulation results revealed that 100% salt rejection can be achieved by using different functional groups for the outer wall CNT membrane with 9 Å, 11 Å, 13 Å and 97.24% for 15 Å interstices. Importantly, the water fluxes through the interstice (9 Å, 11 Å, 13 Å, and 15 Å) of the outer wall CNT membrane with high desalination were 3.43, 4.52, 5.95 and 5.49 times higher of than that of closely packed modified (10,10) CNT membrane with 100% desalination, respectively, implying the great potential of the interstice array of CNT as building blocks for the preparation of next-generation desalination membranes.