Marine vessels rely heavily on propeller shaft systems to adjust the engine torque and propeller thrust. However, these systems are subjected to various dynamic excitations during operation, such as transverse, longitudinal, and torsional excitations. These excitations can arise from factors like non-uniform stern flow fields, misaligned components, and the whirling motion of the shafts, which can affect the integrity and reliability of the vehicle. To analyze the dynamic response of the propulsion shaft system and ensure its reliability, numerical/analytical models are currently in practice. The finite element method (FEM) is a popular choice, but uncertainties in bearings and connectors stiffness lead to inaccuracies in the Finite Element model, resulting in significant differences between the experimental and theoretical models. This paper proposes the response surface optimization (RSO) technique to estimate unknown bearing stiffness in the propulsion shaft system. The experimental model of the propeller shaft system is constructed using steady-state response with step sine excitation. The RSO technique is then used to update the natural frequencies and vibration amplitude of the FE (Finite Element) model. The updated model shows less than a 10% difference in natural frequencies and vibration amplitude compared to the experimental model, demonstrating that the proposed technique is an efficient tool for marine shaft dynamic analysis.