Epoxy joints exhibit shorter curing times and simpler construction compared to wet joints, significantly improving the construction efficiency of prefabricated steel-concrete composite (PSCC) beams. To assess the applicability of PSCC beams with epoxy joints in the negative bending moment regions, a single-point bending test was performed on one PSCC beam with epoxy joints and one ordinary steel-concrete composite (SCC) beam without joints, followed by a comparative analysis of their mechanical behavior. Furthermore, parametric analyses were carried out using a finite element simulation method validated by the tests, focusing on the shape, location, and number of epoxy joints. The results show that the yield and ultimate loads of PSCC beams decreased by 12.1% and 10.4%, respectively, compared to SCC beams. Under prestress, however, the cracking load and ductility increased by 33% and 17.6%, respectively, while sectional rotation performance was enhanced. Moreover, keyed and stepped joints demonstrated better ultimate load capacity and ductility in comparison to linear joints. As the joint location shifted closer to the mid-span and the number of joints increased, both ultimate load capacity and ductility gradually decreased. Design recommendations were provided to offer valuable references for the intelligent construction of PSCC beam bridges with epoxy joints.