We observed Jupiter's infrared aurora using the Subaru Infrared Camera and Spectrometer (IRCS) with adaptive optics, in order to compare horizontal and vertical emission profiles among H3+ fundamental, H3+ overtone, and H2 emissions. The fundamental and overtone lines show similar horizontal distributions around the main auroral oval for both hemispheres. There is no correlation between the fundamental lines and temperature; however, a correlation seems to exist for the overtone lines. Although both the fundamental and overtone lines are related to electron precipitation, there are differences in the precipitating electron energies that influence the emissions, because of their different emission altitudes. In addition, the morphological difference between the H2 and H3+ emission structures is significant. That is, the intensity of the H3+ emission is enhanced around the main oval, but that of the H2 emission is not. The peak altitudes of the H3+ fundamental, H3+ overtone, and H2 are 650, 870, and 830km for the north and 700, 910, and 950km for the south, with the uncertainties of approximately 100km. This finding, that the fundamental emission peak altitude is found to be lower than those of the overtone and H2 emissions, is consistent with the theoretical models and derived temperatures for the emission peak altitude. We also find similar peak altitudes for the H2 and H3+ overtone emissions. This is in accordance with previous observations, which have revealed that the altitude of H2 is higher than the model-based expectation. Collisional de-excitation of H2 can dominate at lower altitudes, which might explain the higher emission peak altitude compared to that of the model.