The properties and applications of ionic liquids (ILs) have been widely investigated when they are confined within nanochannels such as carbon nanotubes (CNTs). The confined ILs exhibit very different properties from their bulk state due to a nanoconfinement effect, which plays an important role in the performances of devices with ILs. In this work, we studied the effect of the charge carried by CNTs on confined ILs inside CNTs using molecular dynamics simulations. In charged CNTs, cations and anions are distributed separately along the radial directions, and the transition of orientations of the cations between parallel and vertical to CNTs occurs by changing the charge state of CNTs. The number of hydrogen bonds (HBs) formed by the confined ILs can be reduced by switching the surface charge of CNTs from positive to negative due to the contact modes between cations and anions as well as the distributions of cations in CNTs. The diffusivities along and vertical to the axial direction of CNTs were found to be non-monotonic owing to the “trade-off” effect from both ion pair interlocking and anchoring ILs on the CNT walls. Additionally, the region-dependent dynamics of ILs were also related to the intermolecular interactions in different regions of CNTs. Furthermore, the vibrational modes of ILs were obviously influenced in highly charged CNTs as determined by calculating the density of vibrational states, which demonstrated the transitions in the structure and interactions. The density distributions changed from single layer to double layers when increasing the pore size of neutral CNTs while the hydrogen bonds exhibited a non-monotonic tendency versus the pore sizes. Our results might help to understand the structure and dynamics of confined ILs as well as aid optimizing the performance of devices with ILs.