The unique seismic response characteristics of the Miaoziping long-span continuous rigid frame bridge with ultra-high piers was investigated. A three-dimensional finite element model was established, and incremental dynamic analysis (IDA) was performed to systematically investigate the dynamic response characteristics under bi-directional and tri-directional seismic excitations. The results indicate that under bi-directional seismic excitation, the main pier exhibits a 43% probability of slight damage at PGA=0.4g. After incorporating vertical seismic excitation, the main pier shows a 22% probability of slight damage at PGA=0.2g, with the exceedance probability of complete damage state increasing by approximately 25%. Regarding the bearing system, the introduction of vertical seismic excitation significantly accelerates the damage progression rate, reaching a 100% probability of slight damage at PGA=0.4g.