Emission mechanism of the magnetars is still controversial while various observational and theoretical studies have been made. In order to investigate mechanisms of both the persistent X-ray emission and the burst emission of the magnetars, we have proposed a model that the persistent X-ray emission consists of numerous micro-bursts of various sizes. If this model is correct, intensity Root Mean Square (RMS) variations of the persistent emission exceed the values expected from the Poisson distribution. Using $Suzaku$ archive data of 11 magnetars (22 observations), the RMS intensity variations were calculated from 0.2 keV to 70 keV. As a result, we found significant excess RMS intensity variations from all the 11 magnetars. We suppose that numerous mircro-bursts constituting the persistent X-ray emission cause the observed variations, suggesting that the persistent X-ray emission and the burst emission have identical emission mechanisms. In addition, we found that the RMS intensity variations clearly increase toward higher energy bands for 4 magnetars (6 observations). The energy dependent RMS intensity variations imply that the soft thermal component and the hard X-ray component are emitted from different regions far apart from each other.