The vertical security problem of maglev train is challenging for nonlinearity, external disturbances, unmeasurable airgap velocity and constrained output. To solve this problem, a semi-supervised controller based on deep belief network (DBN) algorithm is proposed in the presence of unknown external disturbances. Firstly, the extended state observer (ESO) is designed to ensure fast convergence of observation errors with high enough estimation precision. An output-constrained controller is designed by backstepping method, and the estimated value of ESO is introduced to ensure that the output airgap is constrained within a bounded range. Then, the stability of this method is proved based on the symmetric Barrier Lyapunov function. Subsequently, a semi-supervised controller is presented based on DBN algorithm and the output-constrained controller. The numerical simulation results show that this method can effectively deal with unmeasurable airgap velocity and generalized external disturbances, and guarantee the vertical security with output airgap within a bounded range. Finally, experiments are implemented on a full-scale maglev vehicle and the experimental results demonstrate that the developed deep learning controller can ensure the vertical security.