The probability of a structure being or exceeding a specific damage state for various seismic intensities was described by seismic vulnerability. Considering the randomness of ground motion, there existed numerous ground motion intensity measures (IMs) that will affect the dynamic response of tunnel. Therefore, selection of suitable ground motion intensity measures will be of great significance for the seismic design and vulnerability assessment of tunnels. Typical shallow and deep tunnels in soft soil were chosen as examples to study suitable ground motion intensity measure. Numerous nonlinear time-history calculations were conducted using incremental dynamic analysis (IDA) method. Then, the selected 18 IMs were tested for several metrics, i. e. efficiency, practicality and proficiency based on an extended number of logarithmic regression analyses between the IMs and the damage measure (DM) for the examined tunnels in soft soil deposits. The results revealed that the peak ground acceleration (PGA) at the ground surface may be considered as the optimal IM for shallow tunnel, followed by peak ground velocity (PGV), while PGV is the optimal IM for the deep tunnel, followed by velocity spectrum intensity (VSI). This result provides a basis for evaluating the seismic performance of tunnels under different working conditions. It also lays a foundation for further calculation of structural vulnerability of tunnels with different service periods and different structural forms.