An adaptive method for suppressing mechanical vibration of multiple frequencies is investigated. The adaptive controller is reinforced with saturation alleviator to improve the convergence rate and performance of the adaptive algorithm. Tracking filters are used to extract harmonics of fluctuating frequencies and the anti-saturation unit works in series with the tracking filters to give constrained harmonic output. As a result, the controller is insensitive to abnormally large input that would otherwise induce saturation in actuators. A dynamic model is built for vibration suppression simulation and the numerical results indicate that the adaptive algorithm is effective in cases of multiple fluctuating frequencies and output saturation. Experiments were also conducted to test the performance of the adaptive method. Excitation with oscillating frequencies was applied, and the results have demonstrated that the harmonics can be suppressed effectively with the adaptive method.