Many ground motion intensity indexes were used to the structure seismic analysis, but there were no unified final conclusion and lack of systematically analysis on the applicability for these index. The correlation between the ground motion intensity and the structure seismic response was investigated by inputting 100 typical ground motion records to the SDOF system and the seismic-isolation-and-reduction continuous-beam bridge which have different period. The results show that the intensity index can be separated into four groups. The group I index represented by Sa(T1) has a high correlation with different period structure. The group II index represented by PGA has a high correlation with short period structure. The group III index represented by PGD has a high correlation with middle period structure. The group IV index represented by PGV has a stable correlation. The group I index is suggested to used as the ground motion intensity. A practical engineering analysis shows that different intensity indexes have different correlation with the known natural vibration period structure.