To overcome the limitations of conventional control strategies in simultaneously suppressing external sway disturbances and internal parameter variations—induced by strong eddy current effects in marine canned magnetic bearings (MBs)—this paper introduces an improved model reference adaptive control (MRAC) method. First, electromagnetic force and dynamic models of the marine canned MBs are developed, taking into account eddy current effects and oscillatory motion. On this basis, a state observer is designed to estimate the system’s unknown dynamics. A predictive error term is formulated to capture the combined influence of model uncertainties and external disturbances. An adaptive law is then applied to compensate for these unknown dynamics and external disturbances. Moreover, the stability of the marine canned MBs system under the proposed improved MRAC scheme is rigorously analyzed using Lyapunov stability theory. Simulation results confirm the effectiveness of the algorithm, showing that, compared with conventional PID control, the improved MRAC approach reduces rotor vibration by more than 53%, significantly strengthening the disturbance rejection performance of marine canned MBs.