For the structural seismic design and research, the selection of the input ground motions in the seismic fragility analysis is of great significance. However, the conventional ground motion selection methods do not consider the diversity and discreteness of the earthquake group or are not clear enough, which reduces the reliability and significance of seismic fragility analysis. To solve the problem, an innovative input ground motion selection strategy is proposed from the article, based on the response of the simplified model of the target structure under the excitation of the ground motion group, and judges the diversity of the input ground motion group through an improved ground motion intensity measure and the conception of information entropy. A finite element model of a 3-span continuous girder bridge is established as the numerical case study, and the correlation between the information entropy of the simplified model response and the information entropy of the actual finite element model response is verified by implementing the proposed method. The result shows that the strategy is capable of selecting input ground motion group based on its diversity, and it could be utilized as a simple and reliable basis for the analysis and selection of input ground motions in seismic fragility analysis.