In the processes of seismic design of underground structures, selecting a reasonable input ground motion is very important, which can cause severe damage to underground structures. To quantitatively evaluate the seismic damage potential of ground motions on multi-storey underground structures and solve the problem that single intensity measures are inadequate in accurately indicating the seismic damage potential of ground motions, this paper taking the input ground motions in the seismic design of underground structures as the research object, and constructing some composite intensity measures that can effectively characterize the damage potential of input ground motion. Firstly, considering that the underground structures in different characteristic period-type sites will exhibit different seismic responses under the same excitation, the soil–structure system is divided into four-period bands. Then, four representative periods are selected from four-period bands respectively, and the corresponding four soil–structure system numerical models are established. Subsequently, 40 ground motions are selected for elastoplastic numerical analysis, and the results of the numerical analysis were used as sample data to construct composite intensity measures corresponding to soil–structure systems in each period band using the partial least squares regression method. Finally, 100 additional ground motions were used to verify the correlation between the composite intensity measures and the seismic damage of underground structures. The results show that the correlation coefficient between the composite intensity measures and the seismic damage of multi-storey underground structures is better than those of commonly used single intensity measures.