Aircraft wake are a couple of counter-rotating vortices generated by a flying aircraft, which can pose a serious hazard to follower aircraft. The behavior prediction of it is a key issue for air traffic safety management. To this end, we propose a prediction method based on data assimilation, which can be used to predict the evolution and hazard area of aircraft wake vortex from the vortex-core’s positions and circulation. To construct our wake vortex prediction model, we use linear shear and least square estimation. In addition, we use a data assimilation model based on the unscented Kalman filter to instantly correct the predicted trajectories. Our experimental results show that the proposed method performs well and runs steadily, thus, providing an effective tool for aircraft wake vortex prediction and support for the establishment of dynamic wake separation in air traffic management.