A novel vibration damping structure is designed based on the existing package structure of MEMS vector hydrophone. It is desirable that this novel structure can isolate the vibration noise caused by working platform so as to improve the anti-noise ability of hydrophone. This novel structure is made of “dow corning” damping silicone rubber which is manufactured with a certain proportion because of its small Young’s Modulus. The hydrophone is fabricated in the form of original packaging structure firstly and then in vibration-isolation packaging structure. Laboratory tests by means of the shaking table test and standing-wave tube test are performed to validate the theoretical results. The test results prove that the vibration damping structure can effectively isolate the interference signal produced by working platform without affecting the sensitivity of hydrophone obviously.