An unsteady flow phenomenon of clear air turbulence was investigated by numerical simulation integrating flight data of encounters with severe turbulence. To determine the initial condition of the numerical simulation based on the flight data, the four-dimensional variational method was employed. The validation of the present method was conducted by using pseudo flight data that are obtained from a reference flowfield produced by the numerical simulation. Then the four-dimensional variational method was applied to two actual severe turbulence cases to reproduce the flowfield of these turbulent flows. The validation results show reproducibility of the flowfield, even with spatially limited measurement data such as flight data, as long as the data involve primary flow features. Unsteady flowflelds of turbulence were successfully simulated by using the four-dimensional variational method based on two cases of actual flight data. The results show the existence of vortices that correspond to clear air turbulence. In addition, the existing hazard indices F-factor and root-mean-square normal load were applied to the reproduced flowfield to obtain a spatial distribution of these hazard indices.