An ultrasonic nanocrystal surface modification (UNSM) technique with different striking numbers (34,000mm−2 and 69,000mm−2) was employed to modify the surface of plasma-nitrided S45C steel. After the UNSM treatment, the fatigue strength of the 8h plasma-nitrided specimen (N8) was clearly improved, and the sub-surface cracks were nearly restrained, while the 48h plasma-nitrided specimen (N48) showed no improvement of fatigue strength. The mechanical properties of the specimens before and after UNSM treatment were characterized, such as the microhardness, the surface roughness, and the surface compressive residual stress. A grain refinement layer was formed on the surface of the specimens due to the severe plastic deformation induced by the dense striking, and the grain distribution was analyzed by using X-ray diffraction. The grain refinement layer played an important role in the improved mechanical properties. The fatigue limit enhancement mechanism was examined by analyzing the stress intensity factor from fish-eye cracks. For the fish-eye cracks, the stress intensity factor in the facet area, △Kfacet, was found to be a constant value of approximately 4.08MPa·m1/2, regardless of either the UNSM treatment or the nitriding duration.