An unsteady flow phenomenon of clear air turbulence (CAT) was investigated by large eddy simulation (LES) using flight data available from airlines encounter with severe turbulence. To incorporate the flight data into the LES, the four-dimensional variational method (4D-Var) was employed. This paper presents formulation and numerical method of the 4D-Var applied to the flight data. The validation of the present method was conducted using pseudo-flight data obtained from reference flow field. Then, the 4D-Var was applied to two severe turbulence cases. Existing hazard indices, F-factor and root mean square (RMS) normal load were evaluated on the reproduced flow field. The validation results show reproducibility of flow field using limited measurements if the measurements include primary flow features. An unsteady flow of CAT was simulated by using the 4D-Var and the results show the existence of characteristic vortices which correspond to CAT.