It is expected that the off-state leakage current of MOSFETs can be reduced by employing vertical body channel MOSFETs (V-MOSFETs). However, in fabricating these devices, the structure of the Si pillars sometimes cannot be maintained during oxidation, since Si atoms sometimes disappear from the Si/oxide interface (Si missing). Thus, in this study, we used first-principles calculations based on the density functional theory, and investigated the Si emission behavior at the various interfaces on the basis of the Si emission model including its atomistic structure and dependence on Si crystal orientation. The results show that the order in which Si atoms are more likely to be emitted during thermal oxidation is (111) > (110) > (310) > (100). Moreover, the emission of Si atoms is enhanced as the compressive strain increases. Therefore, the emission of Si atoms occurs more easily in V-MOSFETs than in planar MOSFETs. To reduce Si missing in V-MOSFETs, oxidation processes that induce less strain, such as wet or pyrogenic oxidation, are necessary.