Temperature has a significant effect on the performance of the proton exchange membrane (PEM) on the application in the fuel cell. In this study, a functionalized carbon nanotube (CNT) with fluorine was adopted as the one-dimensional channel to simulate the proton conductive channel in the PEM. Molecular dynamics simulations have been carried out to investigate the temperature effect on the structure and hydrogen bond properties of protons in the nanochannel. It was found that increasing temperature lowers the energy barrier of proton along the nanochannel. This implies an easy access and transfer for protons into PEM at high temperatures. The coordination numbers of water and proton decreased as the temperature increased. As a result, the cluster size showed a decreasing tendency, but the cluster length along the channel had little dependence on temperature. The hydrogen bond structure along the axis with fewer branches was beneficial to the effective transfer of protons through the nanochannel. Additionally, the dependence of hydrogen bonding lifetime on temperature suggested that high temperature leads to the frequent breaking and reforming of hydrogen bonds, facilitating proton transfer along the effective hydrogen bond network. This study helps to understand the effect of temperature on the structure of protons in the nanochannel.