Gate insulator of vertical MOSFET (V-MOSFET) is formed by silicon oxide. However, Si pillar cannot keep the structure during oxidation process because the Si atoms disappear from bulk (missing-Si). Moreover, the effect of hydrogen annealing for VMOSFET under the typical condition becomes weaker than that for planer MOSFET. In this study, we revealed the physical origin of missing-Si and hydrogen annealing effects by using first principles calculation method. We considered that the strain which is accumulated at the Si/SiO2 interface in V-MOSFET due to pillar structures. In this study, we clarified the strain dependence of thermal oxidation of V-MOSFET based on the Si-emission model [1,2]. The obtained results indicate that the compressive strain is one of the causes of the missing-Si. Furthermore, we investigated the strain dependence of the effect of hydrogen annealing. As a result, we revealed that hydrogen annealing temperature of VMOSFET should be lower than that of planer-MOSFET.