Abstract: The configuration of the boundary conditions of journal and thrust bearings is one of the most important and difficult parts of the procedure of marine propulsion shaft alignment. Based on the hydrodynamic lubrication theory, the lubrication performance of journal bearings is analyzed with consideration to misalignment. The equivalent deflection of the shaft element obtained from the bearing clearance, the lubricating oil film thickness and the elasticity of the supporting structure are proposed during shaft alignment calculation, and the results of the alignment calculation using the equivalent deflection of the shaft element are compared with the scenarios of the stiff support hypothesis and linearly elastic support hypothesis. The bending moment acting on the thrust collar resulting from the misalignment or uneven distribution of the thrust pads in the circumferential direction is calculated, the influence of the additional moment on the shaft alignment is analyzed, and the coupling procedure of the shaft alignment calculation and bearing lubrication performance calculation is established. The results show the important influences of bearing clearance, lubricating oil film thickness and additional moment on shaft alignment.