The pitch deviation, non-parallel end face, and middle diameter deviation generated during the machining process of connecting rod bolts will lead to changes in bolt preload and stress distribution under ideal conditions, and their effects under individual or interaction are not fully understood. The finite element simulation model of connecting rod bolt tightening was established by Abaqus finite element simulation analysis software. The Yamamoto analysis method verified the finite element model of connecting rod bolts. The effects of pitch deviation, non-parallel end face, and middle diameter deviation on the preload, stress distribution, and fatigue safety factor of connecting rod bolts under tightening load were studied. The results show that increasing pitch deviation and middle diameter deviation or decreasing non-parallel end face will increase the bolt preload under the same torque. When the pitch is 1 mm, the middle diameter is 8.3505 mm, and the non-parallel end face is 0.5°, the fatigue safety factor of the bolt failure area is the largest, and the fatigue failure does not quickly occur during the working process. The bolt connection structure of a U-shaped cutting groove can significantly improve the fatigue strength of the joint between the bolt head and the screw, and its average fatigue safety factor is 1.71.