A constraint based on climatology is introduced to the cost function of the three-dimensional variational assimilation (3dVar) to correct the error of the zonal mean wind structure in the global data assimilation system at Korea Meteorological Administration (KMA). The revised cost function compels the analysis fit to the chosen climatology while keeping the balance between the variables in the course of analysis. The constraint varies selectively with the vertical level and the horizontal scale of the motion. The zonally averaged wind field from European Centre for Medium-Range Weather Forecasts Re-Analysis 40 (ERA-40) is used as a climatology field in the constraint. The constraint controls only the zonally averaged stratospheric long waves with total wave number less than 20 to fix the error of the large scale wind field in the stratosphere. The constrained 3dVar successfully suppresses the erroneous westerly in the stratospheric analysis promptly, and has been applied on the operational global 3dVar system at KMA.