The frictional vibration generated in water-lubricated rubber bearings operating under low speed, heavy load, startup and shutdown conditions can severely degrade the reliability and the sheltered performance of underwater vehicles. The rubber layer of the ship stern tube water-lubricated rubber bearings is easily elastically deformed under certain loads, which affects the damping performance of the bearing system. To explore the effects of thickness, hardness, and concavo-convexity on the damping property of water-lubricated rubber stern bearings, frictional force, vibration, noise, and displacement and deformation of the contact area were studied using a test rig with a transparent glass cylinder. An orthogonal L-9(3)(4)test design was applied accordingly to determine the optimum construction and material parameters of the rubber layer. Orthogonal test results indicate that among rubber layer hardness, thickness, and test block concavo-convexity, the former is most significant in terms of the frictional vibration, followed by the thickness and, finally, the radius of the surface. When the hardness is 65 A, the thickness is 12 mm, and the plate type is concave, the frictional vibration performance of the rubber layer is optimal. More important, based on the static deformation and the dynamic displacement of the rubber, the causes of the frictional vibration and the influence of different materials and structural parameters on frictional vibration were visually analyzed. The overall trends and the mechanism discussed in this research may be considered as a guideline for the design, optimization, and manufacture of water-lubricated bearings.