Bearing preload significantly affects the running performance of a shaft-bearing system including the fatigue life, wear, and stiffness. Due to the mounting error, the bearing rings are often angularly misaligned. The effects of the combined bearing preload and angular misalignment on the fatigue life of ball bearings and a shaft-bearing system are analyzed in this paper. The contact force distribution of angular contact ball bearings in the shaft-bearing system is investigated based on the system model. The system model includes the bearing model, and the shaft model is verified by comparing with the manufacturer’s manual and the results from other theoretical models, with the difference between the results from the present bearing model and manufacturer manual within 3%. The global optimization method is used to replace the Newton–Raphson algorithm to solve the ball elements’ displacements and friction coefficients, which improves the computation efficiency of the system model. The fatigue life of each bearing is evaluated with the consideration of the two preload methods and two angular misalignment cases. The fatigue life results show that the system life at the optimal angular misalignment is more than 1.5 times that without angular misalignment at the low preload value, and this ratio decreases as the preload value increases. The optimal angular misalignment of both the shaft-bearing system and the misaligned bearing is not always consistent, which depends on the preload value and bearing life. Both the constant-displacement preload and constant-force preload do not cause a significant difference in the highest system life. The different misaligned bearings can lead to different highest system lives as the preload value is low.