In this work, the ship propulsion shaft system with cruciform universal coupling is studied. First, based on the analysis of the structure and characteristics of the cross-axis universal coupling, the motion relations and expressions between the components of the universal coupling are established by using the coordinate transformation method. Second, the characteristics of the four submodels of the head mass point element, the end mass point element, the universal coupling mass point element, and other mass point elements are discussed, and the corresponding torsional vibration differential equations of the four submodels are established. On this basis, the mathematical model of the propulsion shafting system and the differential equations of torsional vibration are established by using the modularization method and lumped parameter method. Finally, the torsional vibration modes and response characteristics of the shafts are calculated and analyzed by using the system matrix method when the external load driving torques of the universal coupling, propeller, and diesel engine are considered. At the same time, the correctness of the mathematical model and calculation method is verified by the test and comparative analysis of ship propulsion shafts. It lays a theoretical foundation for further research on torsional vibration characteristics and mechanisms of the ship propulsion shafting system based on universal coupling. Introduction Universal coupling is a common connection component of mechanical shaft system transmission. It is a common mechanism that can be used to transfer motion and torque. Universal coupling has no requirement for neutrality between the two axes connected. It can be used for intersecting, parallel or staggered multiposition relations, and can still ensure the continuous rotation of the two axes connected. Compared with the belt drive and chain drive, universal coupling has the advantages of large transmission range, compact transmission, high transmission efficiency, and convenient maintenance. Therefore, it is widely used in ships, automobiles, lifting and transportation (Avrigean et al. 2015; Chang et al. 2017), engineering machinery, and other equipment. Because of the manufacturing error, assembly error, and the failure to keep synchronous rotation between the driving shaft and the driven shaft in the working process, additional inertia moment of the universal coupling is generated, which causes the vibration of the system and even leads to the fracture of the universal coupling in serious cases.