In industrial fields such as manufacturing and inspection equipment for electronic devices, micro-vibrations need to be suppressed as they deteriorate the performance of equipment. We previously proposed an add-on type active vibration suppression system as a reliable and simple solution for vibrations that affect electron microscopes, which is an application example of a nanometer-order system. The system suppresses nanometer-order vibrations in the structure simulating an electron microscope by controlling the output of high-thrust piezoelectric actuators using acceleration sensors. However, if the output of the actuator exceeds a maximum limit due to large vibrations, the active vibration suppression system causes a high-frequency disturbance that deteriorates equipment performance. In this paper, we propose a multi-scale vibration control method which estimates the amplitude of the controller output in real time and adjusts the feedback gain on the basis of the estimated amplitude. The proposed method can suppress a wide range of vibrations from nanometer-to micrometer-order, thereby suppressing vibration and stabilizing the active vibration suppression system. The vibration suppression performance of the proposed system is evaluated through experiments using a structure simulating an electron microscope.