To evaluate the seismic fragility of bridges with and without isolation bearings, the numerical models of a three-span concrete box-girder bridge with lead rubber isolation bearings and with non-isolation pot rubber bearings were established. The maximum displacement responses of pier top and bearing under different earthquakes were first analyzed. Then a damage index named ductility ratio of rotation angle was defined to estimate the seismic fragility of bridge piers and bearings. Finally, the wide-bound method was applied to analyze the seismic fragility of bridge system. The analysis results demonstrated that the bearing is the most vulnerable component, and the fragility of the bridge system is greater than pier and bearing. The failure probability of lead rubber bearing is obviously lower than that of non-isolation pot rubber bearing, thus it can be seen that the isolation bearing can effectively reduce the maximum displacement of pier top under earthquake, and the seismic vulnerability of pier with isolation bearings is better than that with non-isolation bearings.