The embedded shear connector with flanges (ESCF) exhibits excellent shear performance in the steel–concrete composite beam. The ESCF consists of embedded corrugated steel web as the shear connector and shape-matched flanges for construction convenience. However, previous research showed that the steel flange of the ESCF was prone to local buckling when subjected to shear force, resulting in insufficient shear strength of the connector. In this paper, head studs were adopted to reinforce the ESCF at the flange with a large width-to-thickness ratio. Nine stud-reinforced embedded shear connectors with flanges (SR-ESCF) were manufactured to conduct the push-out test to investigate the shear performance of SR-ESCF. The effects of the reinforcing studs, thickness of the web, width-to-thickness ratio of the flange, embedding depth of the web, and diameter of the combined rebar on shear strength of the SR-ESCF were revealed and discussed thoroughly. The push-out test results showed that the head studs significantly improved the initial stiffness and load-bearing capacity of the ESCF, which were increased by 17% and 15%, respectively. Moreover, the head studs prevented local buckling of the steel flange. The shear strength of the specimens was greatly influenced by the embedding depth of the web, the width-to-thickness ratio of the flange as well as the reinforcing studs. However, the diameter of the combined rebar and thickness of the web had negligible effects on the shear capacity of the SR-ESCF. According to the test results, the nonlinear finite element model (FEM) and the shear capacity of SR-ESCF prediction formula were created and verified. Furthermore, the layout of the reinforcing studs welded on the flange of the SR-ESCF was optimized by the validated FEM, which indicated that the shear-bearing capacity of the SR-ESCF could be significantly increased by adding studs on the steel flange near the original studs. This research will be of great significance to the design and implementation of the steel–concrete composite beam bridge with corrugated steel web.