Development of high-efficiency and low-cost seawater desalination technologies is critical to solve the global water crisis. Here we report a fast water filtering method with high salt rejection by aligned carbon nanotubes arrays (CNTA). In this study, the effect of interval on the desalination of CNTA was investigated by molecular dynamics (MD) simulation, and our simulation results have shown that water permeation and salt rejection could be greatly improved by the optimization of aligned CNTA membrane. High water permeation could be achieved by specific gap size between highly ordered CNTA, meanwhile, due to high free energy barrier for Na+ passing through the interval of CNTA, high salt rejection could also be achieved. Our study possibly provides a new idea to utilize CNTA membrane for desalination. (C) 2016 Elsevier B.V. All rights reserved.