Effect of carbon nanotube (CNT) shape on desalination efficiency was investigated by computer simulation. Three shapes of CNT including tubular, cone, and hetero-junction (a combination of two different diameter CNTs which connected by a diverged CNT) shaped were simulated at high pressure (>50 MPa). For the first time, we placed neutral charge CNT between two inert walls to illustrate support of CNT that is an inert polymer. Cone shaped CNT conducted water-4 times faster than (6,6) CNT and rejected the ions similar to (6,6) CNT. Actually, cone shaped CNT possesses the shorter residence time and higher number of water in the tube. This is because of the higher capacity and lower energy barrier against water to pass through it. However, hetero-junction CNT showed a slower water conductance because of the formation of water cluster at the large end of CNT that implies a high-energy barrier against water. In addition, H-borid number is also responsible for energy barrier. H-bond number in bulk of water is 4 and should be decreased to 2 to penetrate in the tubular and hetero-junction shaped CNT. Nevertheless, in a cone shaped CNT H-bond number falls down to 3 only at the entrance of the tube. (C) 2016 Elsevier B.V. All rights reserved.