Underwater rock drilling rod method is a simple and efficient technique for rock breaking and reef clearing. However, the vibration of rock and soil layer caused by the instantaneous release of powerful energy of drilling impact will spread to adjacent structures, thus weakening their normal service ability. Based on the reef clearing project of Guangzhou Liquefied Natural Gas Emergency Peak Shaving Gas Station supporting wharf engineering, the vibration response of embankment induced by underwater drilling was explored through field test. The test results show that during the underwater drilling progress, the vibration velocity response of the embankment quickly reaches the peak and then gradually decays. The embankment vibrates continuously 0.2 ~ 0.5 s during the implementation of one single underwater drilling. The closer to the drilling point, the more timely the vibration response is, and the faster the response decays. The peak vibration velocity of the embankment decreases with the increase of the distance between the embankment and drilling point. The vertical vibration attenuation is the most significant, and the vibration attenuation in the perpendicular direction of the embankment is weak. As a result, the embankment tends to move towards its perpendicular direction. The peak vibration velocity of the embankment increases with the increase of the drop hammer height, however, the vibration response of the embankment increases inconspicuously until the drop hammer distance increases to a certain height. Referring to the calculation formula of underwater blasting safety distance of adjacent structures, one practical calculation method of vibration velocity peak value due to the underwater drilling operation is presented by solving the underwater motion equation of the drilling hammer.