A long transmission shaft is typically constructed by connecting multiple shafts through couplings. Joining two non-collinear shafts causes misalignment, which is one of the primary faults in the shaft system. The flexible coupling can compensate for the misalignment up to some extent. However, in this process, the system dynamics may be affected by the coupling characteristics. The present research proposes flexible disk coupling in a misaligned propeller shaft. The coupling is modeled by segmenting the disk into multiple viscoelastic links exhibiting restoring and dissipating behavior. A combination of parallel and angular misalignment is taken to obtain coupling characteristics. Finite element formulation considering the Timoshenko beam theory is applied to obtain the laminated composite shaft equation, and coupling characteristics are integrated. Operator based constituted relationship is utilized to incorporate material damping of both the shaft and coupling. The stiffness and damping of the coupling rotate with the spin synchronized rotor frame and modify the overall system matrices. Therefore, the coupling influences the modal characteristics and response of the rotor shaft system. A comparative study between the coupled and the uncoupled shafts is performed based on the eigenvalue analysis to show the effect of coupling behavior.