The dynamic characteristics of a continuous rigid-frame bridge with fabricated super-high piers (CRFB-FSP) connected by grouting sleeves and adjacent continuous beam bridges (AB) are significantly different, and they are prone to pounding under earthquake excitation. At present, the pounding response between the CRFB-FSP and AB is still unclear, and the impact of the pounding on the seismic performance of a CRFB-FSP is still in the exploratory stage. In this study, two 1/20 scaled models of a CRFB-FSP (MB) and a cast-in-place AB were designed and manufactured. Then, according to the research purpose and the output performance of the shaking table, three each of non-long-period (NLP) ground motions and near-fault pulse-type (NFPT) ground motions were selected as the inputs of the excitation shaking table test. The peak ground acceleration (PGA) changes from 0.5 g to 1.5 g. According to the similarity ratio (1/20), the initial gap between the MB and AB was taken as 7 mm (prototype design: 140 mm). Furthermore, the longitudinal pounding response between the CFRB-FSP and AB, as well as its influence on the seismic performance of the CFRB-FSP, was systematically investigated through a shaking table test and finite element analysis (FEA). The results showed that the pounding with the CRFB-FSP easily caused a persistent pounding, which may increase the damage risk of the pier. The peak pounding force under the NFPT ground motion was more significant than under the NLP ground motion, whereas the pounding number under the NFPT ground motion was smaller. The peak pounding force increased with the increase in the initial gap, pounding stiffness, span, and pier height. With and without pounding, the CRFB-FSP reflected higher-order mode participation (HMP) characteristics. After pounding, under the NFPT excitation, the HMP contribution increased significantly compared with that of the without pounding condition, while this effect under the NLP excitation was smaller. The peak displacement of the main beam of the CRFB-FSP increased with the increase in the main beam span, pier height and initial gap. The peak bending moment of the pier bottom increased with the increase in the main beam span and initial gap, however, decreased with the increase in the pier height. Moreover, the peak displacement of the main beam and the peak moment of the pier bottom of the CRFB-FSP both reduced. In contrast, the corresponding seismic response of the AB increased under the same conditions.