Reinforced concrete structures are frequently subjected to impact loads during their service life, leading to complex dynamic responses that are often difficult to predict. Scaling test provides an essential methodology for studying impact resistance and analyzing dynamic behaviors. However, studies have revealed that geometrically similar structural under dynamic loading often exhibit scaling effect—their dynamic response deviate from classical scaling laws even when geometric feature are satisfied similarity criteria. The underlying mechanism of these scaling effect in geometrically similar RC beams under impact loads remains unclear. This study aims to systematically investigate the influence of concrete heterogeneity on the impact response and scaling effect of geometrically similar RC beams. Using a comparative analytical approach, three numerical models were established: a homogeneous RC beam (Homogeneity) and two heterogeneous RC beams (Heterogeneity-I and Heterogeneity-II). The displacement, impact force, and reaction force were compared. Furthermore, damage modes, deflection curves, and energy absorption characteristics were analyzed to explore the intrinsic mechanisms of scaling effect. The results indicate that the concrete heterogeneity is one of the factors contributing to the scaling effect in the displacement response of geometrically similar RC beams, while its influence on impact force and reaction force is relatively minor. The intrinsic mechanism of the above phenomenon may be the difference in damage modes due to heterogeneity, which enhances the local response of the RC beams with analysis of deflection curves and energy absorption. Additionally, within the scope of this study, higher impact velocities lead to more pronounced scaling effect in the displacement response. These findings provide theoretical insights for impact-resistant design of concrete structures and for similitude analysis in scaled experimental studies.