In this study, flexible transportation system which is obtained by combining linear motor and 4-pole type yoke hybrid electromagnet is analyzed using 3D Finite Element Method (FEM) in order to achieve magnetic levitation force and torque characteristic. Linear system model is derived corresponding to 3-axis motion dynamic of the system by considering the analysis results. The hybrid electromagnet inherently has a non-linear characteristic and from the point view of controllability, it is unstable. In order to control the system, state feedback integral controller is designed using the pole assignment method by considering the state of the excitation voltage for each axis. Controller poles are determined using coefficient diagram method (Canonical polynomial method). Magnetic levitation system includes sensors that measure only the air gap. In order to estimate other states of the system, the disturbance observer is designed to obtain states and disturbance input for each axis and is estimated and integrated into the control loop. The estimated disturbance value is factored by the appropriate conversion gain and added to the input signal of the plant, so that the robust control system is achieved. Experimental results have shown effectiveness of the proposed control algorithms.