A vibration suppressing device for a spacecraft. A plurality of spacecraft deflection sensors measure a plurality of spacecraft deflections at specified locations on a spacecraft structure. A spacecraft modal coordinate calculation unit calculates a plurality of spacecraft modal coordinates. A high pass filter extracts a plurality of fluctuations of spacecraft modal coordinates. A cost function calculation unit calculates a cost function as a function of the plurality of fluctuations of spacecraft modal coordinates. A payload position calculation unit calculates an optimal payload position minimizing the cost function. A payload position adjustment device generates a control input suppressing a vibration transmitted to the payload system, and adjusts the payload position to the optimal payload position.