The ion-ion instability is excited in an ion beam plasma system. It is found that the ion-ion instability is effectively suppressed by RF pumps with frequencies close to or higher than the peak frequency of the instability. These results are compared with the prediction of the Van der Pol equation to clarify the physical mechanism of the suppression of the ion-ion instability by the RF pumps. It is shown that the suppression mechanism around fex/fii approximately=1 is synchronous suppression whose tendency is similar to the prediction of Van der Pol equation, and the mechanism at fex/fii>1 is due to the perturbation of the ion beam energy caused by the RF pumps.