From a manufacturing viewpoint, the manufacturing tolerances of a hydrodynamic journal bearing system are inevitable. To examine and understand the effect of manufacturing tolerances on dynamic characteristics of a hydrodynamic journal bearing system can help engineers to confidently choose reasonable tolerances at design stage or to enable the system with certain manufacturing tolerances to operate closer to the theoretical predictions. This study presented a theoretical analysis method to determine and demonstrate the effect of manufacturing tolerances on bearing stiffness and damping, in which the concepts of limits, tolerances and nominal dimensions are introduced in. The results show that the manufacturing tolerances of a hydrodynamic journal bearing system have profound influences on the bearing stiffness and damping, and the magnitude of effect depends on system design parameters in the form of Sommerfeld number. The presented method will better predict system stiffness and damping characteristics.