In order to accurately evaluate the seismic damage of shallow buried utility tunnel under near-fault ground motion, ABAQUS is used to establish the finite element model of whole soil-structure, while the analysis of seismic fragility of structure is conducted based on the incremental dynamic analysis (IDA) method with the maximum of inter-story displacement angle of utility tunnel as the damage measure, and the influence of both the intensity measure of near-fault ground motion and the characteristics of site soil on the seismic performance of utility tunnel is investigated. The results show that the dispersion of acceleration-type measure of near-fault ground motion is the least, and it is suggested that peak ground acceleration (PGA) and spectral acceleration (Sa) in the acceleration-type measures should be selected as the intensity measures of ground motion. The back propagation (BP) neural network can be used to effectively predict the seismic damage of utility tunnel structure with the calculated data by finite element method as samples, and the PGA, Sa and shear modulus of soil all have great influence on the seismic fragility of utility tunnel. Meanwhile, the exceedance probability gradually decreases with the increase of the shear modulus of soil. The variation range of exceedance probability at Life Safety (LS) or Collapse Prevention (CP) performance level is significantly greater than that at Operational (OP) or Immediate Occupancy (IO) performance level. Considering that double parameters of PGA and Sa can more accurately reflect the effect of the different ground motion parameters on structural damage, and considering single parameter of PGA or Sa may overestimate the damage degree of structures, it is suggested that both PGA and Sa should be considered for the analysis of seismic fragility of shallow buried underground structures such as utility tunnel.