It is of the utmost importance to highlight the necessity of characterizing the operational stabilities of vertical-channel thin-film transistors (VTFTs) using In-Ga-Zn-O (IGZO) channel layers as potential back-plane devices for larger-area and higher-resolution display applications. To elucidate the structural variations in channel structures, the device characteristics of the mesa-shaped VTFT were compared with those of the conventional planar-channel TFT (PTFT). The results demonstrated that there were no significant differences in positive-bias stability between the VTFT and the PTFT. Nevertheless, under negative-bias-illumination stress (NBIS), VTFTs and PTFTs exhibited quite distinct instability behavior. The results were suggested to be attributed to the photo-ionization of oxygen vacancy (VO) initiated under illumination stress below a given wavelength. To ascertain the discrepancies in operational behaviors between the two devices, the shift in turn-on voltage (ΔVON) and the change in subthreshold swing (ΔSS) were examined with a lapse of stress time. The ΔVON values were +0.11 V and +0.18 V for the PTFT and VTFT, respectively, under a stress of −2 MV/cm for 3600 s in a dark state. In contrast, under the same conditions with a blue wavelength, they were −0.45 V and −1.81 V, respectively. A larger negative ΔVON for the VTFT was suggested to result from a larger amount of intrinsic defects, such as VO, which originated from the rugged back-channel corresponding to the vertical sidewall of the spacer pattern. The defect-related carrier (DRC) generation may result in a higher degree of VO photo-ionization for the VTFT. As a result, the VTFT showed a positive ΔSS of +120 mV/dec, in contrast to the PTFT, which showed a ΔSS close to zero. This scenario was verified by evaluating the subgap density-of-states within the atomic-layer-deposited IGZO channels for both devices using the thermally-activated electron model. The findings provide valuable insights for the accurate evaluation of the NBIS instability of the IGZO VTFT.