The invention discloses a brake device of a vacuum pipeline wheel rail train, which at least comprises a brake disc, a clutch a, a belt pulley a, a transmission belt, a tensioning mechanism, a belt pulley b, a speed change gear box, a clutch b, a magnetic coupling, a magnetic suspension bearing, a flywheel, a vacuum cavity and a cooling device, wherein the clutch a and the clutch b are automatically controlled by a computer; during braking, the clutch b is jointed with the magnetic coupling firstly, then the clutch a is combined with the brake disc, an axle drives the flywheel to rotate through the transmission belt and the speed change gear box, and the kinetic energy of the axle is changed to the kinetic energy of the flywheel; when the rotating speed of the flywheel reaches the maximum value, the clutch a is disconnected from the brake disc, the clutch b is disconnected from the magnetic coupling, and the flywheel still rotates at a high speed; and when the train starts, the clutch a is combined with the brake disc firstly, then the clutch b is jointed with the magnetic coupling, the kinetic energy of the flywheel is transferred to the axle through the gear box and the transmission belt, and thus the braking energy is changed to traction power.