This paper investigates the control problem of magnetic levitation system, in which velocity feedback signal is influenced by stochastic disturbance. Firstly, single-degree-freedom magnetic levitation is regarded as an energy-transform action device. From the view of energy-balance relation, the magnetic levitation system is transformed into port-controlled Hamiltonian system model. Next, based on the Hamiltonian structure, the control law of magnetic levitation system is designed by applying Lyapunov theory. Finally, the simulation verifies the correctness of the proposed results.