Since the discovery of carbon nanotubes (CNTs), they have attracted extensive attention from scholars in various fields because of their excellent properties. The hollow-structured CNTs are often regarded as conduits and containers, which can act as nano-channels for various molecular substances in the membrane structure. As a source of life, water is indispensable to any living organism. In the application of carbon nanotubes as nanochannels, the most important is the ability of carbon nanotubes to store and transport liquids, especially nanoscaled aqueous solutions. Water molecular clusters in confined spaces exhibit unusual structures and properties. The study of special water structures in carbon nanotubes is of great theoretical importance in chemistry, biology and materials science. There are great difficulties in making the experiment on a nanoscale, but molecular dynamic simulation enables us to better study and analyze the structure and properties of water in confined space of CNT on a nanoscale. One has also studied the influence of temperature on the structure of water, but there are few studies focusing on the effect of temperature on the structure of water in confined space. Therefore, molecular dynamics simulation is used to investigate the effects of CNT diameter, CNT chirality and temperature on the water structure and distribution in a confined space. The simulation calculation is completed by GROMACS, the SPE/C water model is used for water molecules, and GROMOS96 54a7 force field is used. Because of the presence of carbon nanotubes, water molecules tend to line up against the walls of the tubes, both inside and outside. In addition, water molecules tend to form highly ordered multi-ring structures in the carbon nanotubes with a size of 1.018–1.253 nm at a certain temperature. It is difficult to form the ordered structure of water in the outer carbon nanotubes. In the above range, with the increase of pipe diameter, the structure of multi-element ring water changes from three-element ring to six-element ring. On the one hand, the ordered structure depends on the diameter of the carbon nanotube, but the chirality of the carbon nanotube does not have a great influence on it. On the other hand, the stability of the ordered structure is temperature-dependent, and the ordered structure of multiple ring water in the carbon nanotube with a larger diameter is more likely to disappear with the increase of temperature. The van der Waals potential distribution is calculated by Multiwfn, and it is concluded that the van der Waals potential inside the tube is extremely low, resulting in a very large dispersion effect, and molecules can spontaneously move from the outer area to the tube. The van der Waals potential can also be negative outside the tube. This explains why water molecules tend to line up against the wall of the tube.