The invention provides a dynamic wireless charging automatic alignment system based on the electric bus stopping process and a controlling method thereof. Automatic alignment of vehicle-mounted wireless charging equipment with a ground charging coil group is achieved in the dynamic processes of pulling in a station, stopping and pulling out the station of an electric bus, and high-efficiency wireless charging is conducted. Through receiving and transmitting signals of a high-frequency coil group, a motor is controlled after the signals are analyzed through a single chip computer to drive the vehicle-mounted wireless charging equipment to move, automatic alignment of the wireless charging equipment is achieved, wireless charging with the maximum efficiency is pursued, the cruising ability is further improved, the number of batteries carried is reduced, and the vehicle body is lightweight. At the same time, through a pulling-in and pulling-out sensing coil group, the single chip computerconducts calculating and analysis and controls timely opening and closing of the alignment system, energy saving and environmental protection are achieved, and safety of the charging system is improved.