For some research vessels, a sonar is installed in the moonpool, and some acoustic detection equipment are installed on the ship bottom behind the moonpool, which helps to avoid the impact of the high-speed flow. The moonpool causes the ship bottom discontinued, forming a particular shear layer oscillation. The shear layer oscillation affects the bubble generation and motion in and behind the moonpool. The sonar and acoustic equipment will malfunction when surrounded by many bubbles. However, there is almost no research on the shear layer oscillation near the moonpool. So, in this paper, by measuring the pressure near the moonpool and monitoring the fluid motion in the moonpool and bubbles’ distribution along the ship bottom, the shear layer oscillation near the moonpool is studied experimentally under the action of the incident current and wave. Furthermore, the effects of the sonar and the moonpool shape are investigated. It can be seen that the shear layer oscillation excites the fluid motion in the moonpool. The sonar forms a complicated boundary in the moonpool, resulting in the increase in the frequency of the shear layer oscillation. The shear layer propagates along the ship bottom in the form of the ship bottom wave. Clarifying the oscillating characteristics of the shear layer along the ship bottom with a moonpool is conducive to the design of moonpools in the research ships, and the detection instruments are arranged in the right place along the ship bottom, so as to make sure the detection instruments work properly and detect the marine environment more accurately.