In order to meet the requirements of accelerated bridge construction (ABC), the structure of steel–concrete composite bridges presents a development trend of the entire assembly. A Prefabricated Composite Shear Studs (PCSS) is proposed to speed up the assembly efficiency of traditional steel–concrete composite beams and improve the effectiveness of the prestress of prefabricated concrete decks in the negative moment zone. A finite element model (FEM) of the PCSS shear connector is established by considering the stress characteristics of different assemblies, thirty different steel tendon quantities, and relative arrangements are selected to analyse the impact of longitudinal prestress on the shear resistance of PCSS, the effectiveness of finite element model is verified this through test results. It is revealed that the steel tendon arrangement and quantity will change the shear resistance of the PCSS shear connectors. However, the magnitude, positive and negative effects are related to the position of the steel tendon along the deck height. When the steel tendon deviates downward from the neutral axis of the deck, the shear bearing capacity and shear stiffness increase; in addition, its force transfer mechanism is that the longitudinal prestress changes the lateral restraint effect of the PCSS on the concrete. Under the combined action of prestressing and transverse restraint of steel plate, the cooperative working ability of the stud and surrounding concrete can be enhanced or weakened. Thus, the yielding of stud and concrete damage can be delayed or accelerated, significantly affecting the shear bearing capacity and stiffness.