<p>In practical engineering applications, to prevent buckling instability of the steel web in steel–concrete composite beams, a large number of stiffeners are required. This results in low material utilization, and the residual stresses generated from welding the stiffeners reduce the fatigue life of the steel beam. To overcome the aforementioned challenges, this study develops an innovative prefabricated composite beam system wherein clustered shear bolt connectors are welded onto high buckling-resistant corrugated steel beams. These beams are integrated with precast ultra-high-performance concrete (UHPC) slabs, followed by the incorporation of post-cast shear pockets, thereby substantially enhancing the composite interaction between steel and concrete components. Fatigue tests were conducted on 5 corrugated web H-shaped steel–prefabricated UHPC composite beams. The findings indicate that a moderate shear connector arrangement provides reliable shear resistance while maintaining flexural stiffness under fatigue loading. A lower degree of shear connection not only accelerates the propagation of fatigue damage in the shear studs but also triggers an earlier and more rapid increase in beam-end slip, thereby affecting the overall stiffness and flexural performance of the composite beam. A fatigue crack propagation model for the fatigue defect in the corrugated steel web beam was proposed using fracture mechanics theory.</p>