The purpose of this paper is to present a framework to analyze the interaction between an actively controlled magnetic levitation vehicle and a guideway structure under gusty wind. The equation of motion is presented for a 30-dof maglev vehicle model consisting of one cabin and four bogies. In addition, a lateral electromagnetic suspension (EMS) system is introduced to improve the running safety and ride quality of the maglev vehicle subjected to turbulent crosswind. By using the developed simulation tools, the effects of various parameters on the dynamic response of the vehicle and guideway are investigated in the case of the UTM maglev vehicle running on a simply supported guideway and cable-stayed guideway. The simulation results show that the independent lateral EMS and associated control scheme are definitely helpful in improving the running safety and ride quality of the vehicle under gusty wind. In the case of the cable-stayed guideway, at low wind speed, vehicle speed is the dominant factor influencing the dynamic responses of the maglev vehicle and the guideway, but at wind speed over 10 m/s, wind becomes the dominant factor. For the ride quality of the maglev vehicle, wind is also the most influential factor.