Novel and complex nanostructures of amphiphiles assemblies facilitate realizing of many practical applications in nanotechnologies. Under different physical conditions, amphiphiles can form various morphologies. In this article, the self -assembly of bolaamphiphiles was investigated under the cylindrical confinement of carbon nanotubes by coarse-grained molecular dynamics simulation. We found that bolaamphiphiles inside a carbon nanotube with a relatively large diameter tended to self-assemble into curved cylindrical micelles, and further some of these micelles can form double helix structures which were not observed in bulk solutions. We develop an effective method to characterize different morphologies. Our analysis results showed that the formation of double helix and other amorphous morphologies of micelles in carbon nanotubes is not induced by the conformational variation of bolaamphiphiles. Moreover, through examining the potential energies of different structures, we infer that it is entropy which leads micelles to bend even to form double stranded helix structures. In addition, we analyzed the sizes of micelles and find the scission and recombination of micelles during the double helix formation process. This work indicates that the confinement of carbon nanotube is an available method to produce complex nanostructures and provides some new insights of the self-assembly of bolaamphiphiles.