We resolved the vertical emissivity profiles of H3+ overtone, H3+ hot overtone, and H2 emission lines of the Jovian northern auroras in K band obtained in December 2011 observed by the IR Camera and Spectrograph of the Subaru 8.2 m telescope with the adaptive optics system (AO188). The spatial resolution achieved was ~0.2 arcsec, corresponding to ~600 km at Jupiter. We derived the vertical emissivity profiles at three polar regions close to the Jovian limb. The H3+ overtone and H3+ hot overtone lines had similar peak altitudes of 700–900 km and 680–950 km above the 1 bar level, which were 100–300 km and 150–420 km lower, respectively, than the model values. On the contrary, the H2 peak emission altitude was high, 590–720 km above the 1 bar level. It was consistent with the value expected for precipitation of ~1 keV electron, which favors a higher‐altitude emissivity profile. We concluded that the lower peak altitudes of H3+ overtone and hot overtone lines were caused by the nonlocal thermodynamic equilibrium effect stronger than the model assumption. We could reproduce the observational emissivity profiles from the model by including this effect. It has been proposed that neutral H2 and ionized H3+ emissions can have different source altitudes because of their different morphologies and velocities; however, our observed results with a general circulation model show that the peak emission altitudes of H3+ and H2 can be similar even with different velocities. Key Points Vertical emissivity profiles of Jovian IR aurora were resolved in K band H3+ overtone and hot overtone lines had lower peak altitudes than the model This lower peak was caused by the non‐LTE effect stronger than the model