This paper presents the design and application of a novel active damping and disturbance rejection controller for a magnetic levitation stage. Feedback linearization, based on the rigid-body dynamics of the levitated stage, and force distribution, based on a time-varying force distribution matrix that takes six-axis motion of a floater into account, are adopted to establish a decoupled and linearized dynamics between the six inputs and the six-axis motion. By integrating an augmented state estimator that provides full state and disturbance estimation, a linear controller that provides active damping for each axis is designed, providing the whole controller with active damping and disturbance rejection capability. In addition, the parameters of the designed controller can be easily selected based on the desired damping and natural frequency, while the parameters of the augmented estimator can be determined according to the desired estimator bandwidth and first system resonance, which make the parameter tuning have a clear physical meaning. Finally, the designed controller was implemented in a field programmable gate array-based control system. Experimental results of the proposed controller and comparison with the previously designed controller are provided to illustrate the feasibility and effectiveness of the designed control algorithm.