In the propulsion shaft systems, the bearings could support the complicated load conditions due to the unbalanced magnetic pull of the motor together with the propeller thrusts. The contact characteristics and skidding behaviors of balls could aggravate. The previous dynamic models of individual ball bearings subjected to the constant load cannot accurately simulate the phenomenon. To overcome this problem, a tribo-dynamic model of a flexible propulsion shaft system is proposed. The real-time contact characteristics and skidding and spinning behaviors of bearings for a propulsion shaft system are calculated based on Newmark-β and Runge–Kutta methods. The bearings’ power losses are numerically estimated. The main power loss components for the system in different rotation speed conditions are located. The effects of the preload and bearing structural parameters (raceway radius, number of balls, initial contact angle) on the bearings’ power losses are discussed. The results indicate that applying appropriate preload on the supporting bearings and reducing the ball number of thrust bearings can be efficient methods for system power loss reduction.