Vibration analysis and control are the main issues of heavy buoyancy regulators, which can improve the runtime performance and reduce the power loss. It is an effective approach to add rubber-based isolators to control the vibrations of the heavy buoyancy regulator. However, the vibration reduction effect of the rubber-based isolators is closely related to their structures and material performance. In this study, according to the geometrics of the connecting components, the structures of the rubber-based isolators are designed by using the vibration theory. The rubber-based isolators with different structures and hardness are considered in the finite element models, whose results are used to achieve the optimal design cases. The vibration isolation transmissibility and static deformation ratio of the rubber-based isolator are discussed. The frequency–displacement characteristics of the heavy buoyancy regulator are also analyzed. The results show that the two presented rubber-based isolators can be used to control the vibrations of the heavy buoyancy regulator. It seems that the presented method can be used for the vibration analysis and control of the heavy buoyancy regulators in underwater vehicles.