Abstract The behavior of carbon impurities in deuterium plasmas and its impact on thermal confinement were investigated in comparison with hydrogen plasmas in the Large Helical Device (LHD). Deuterium plasma experiments have been started in the LHD and high-ion-temperature plasmas with central ion temperature (T _i) of 10 keV were successfully obtained. The thermal confinement improvement could be sustained for a longer time compared with hydrogen plasmas. An isotope effect was observed in the time evolution of the carbon density profiles. A transiently peaked profile was observed in the deuterium plasmas due to the smaller carbon convection velocity and diffusivity in the deuterium plasmas compared with the hydrogen plasmas. The peaked carbon density profile was strongly correlated to the ion thermal confinement improvement. The peaking of the carbon density profile will be one of the clues to clarify the unexplained mechanisms for the formations of ion internal transport barrier and impurity hole on LHD. These results could also lead to a better understanding of the isotope effect in the thermal confinement in torus plasma.