Tornadoes have resulted in significant fatalities and property damage each year. To mitigate this natural hazard, the research on numerically simulating tornadic wind field and investigating the wind effects on civil structures has been conducted. Considering that the setup of the boundary conditions has a significant influence on the generated wind flow when conducting CFD simulations, this study is to investigate how the sizes of the pressure outlet and velocity inlet affect the characteristics of the generated tornadic wind flow by taking the CFD simulation of a real-world tornado (Tornado Spencer) as an example. Based on the observations in this study, the way to improve the tornado simulation by adjusting physical boundary condition is proposed.