Aerodynamic brake is a clean and environmentally friendly braking mode, which does not use mechanical friction as a braking force. This paper describes the development of a small-distributed aerodynamic brake prototype, including its structure, working principle, ground test, and test results. A computational fluid dynamics (CFD) method is developed to obtain the aerodynamic forces of the prototype, and the simulation results are validated by performing a wind tunnel test. On the basis of the CFD simulation, the panel opening process and braking process are modelled to analyse the vertical dynamic characteristics of a high-speed electromagnetic suspension maglev with aerodynamic brakes. In addition, a vehicle, guideway, and levitation controller are modelled. Finally, a three-car system dynamic model is solved to obtain the influences of the opening time, initial braking position, and feedback gains. The aerodynamic forces of the first car show the most significant changes when the braking panels are opened. The increase in the longitudinal force is 15461.16N, and the vertical force varies from a lift force of 35342.98N to a downforce of 40721.35N. The maximum guideway deflection decreases as the opening time increases. The difference between the deflections obtained at opening times of 0.064 s and 0.6 s is 1.2 mm. Furthermore, vertical accelerations decrease as the opening time increases. The condition in which the vehicle brakes when the first car enters the object guideway has the largest influence on the deflection of the guideway. To ensure levitation stability influenced by the vertical change of the first car, a high feedback gain for the levitation clearance change is required. However, the levitation stability with aerodynamic brakes is weakly affected by the feedback gains for the observed velocity and acceleration of the system.